Methods for modifying flowering phenotypes

ABSTRACT

Recombinant polynucleotides and methods for modifying the phenotype of a plant are provided. In particular, the phenotype that is being modified is a plant&#39;s flowering time or flowering period. The method comprises altering the levels of a transcription factor that is introduced into the plant or that is endogenous to the plant.

FIELD OF THE INVENTION

[0001] This invention relates to the field of plant biology. More particularly, the present invention pertains to compositions and methods for phenotypically modifying a plant.

BACKGROUND OF THE INVENTION

[0002] Transcription factors can modulate gene expression, either increasing or decreasing (inducing or repressing) the rate of transcription. This modulation results in differential levels of gene expression at various developmental stages, in different tissues and cell types, and in response to different exogenous (e.g., environmental) and endogenous stimuli throughout the life cycle of the organism.

[0003] Because transcription factors are key controlling elements of biological pathways, altering the expression levels of one or more transcription factors can change entire biological pathways in an organism. For example, manipulation of the levels of selected transcription factors may result in increased expression of economically useful proteins or metabolic chemicals in plants or to improve other agriculturally relevant characteristics. Conversely, blocked or reduced expression of a transcription factor may reduce biosynthesis of unwanted compounds or remove an undesirable trait. Therefore, manipulating transcription factor levels in a plant offers tremendous potential in agricultural biotechnology for modifying a plant's traits.

[0004] In order to maximize reproductive success, plants have evolved complex mechanisms to ensure that flowering occurs under favorable conditions. Analysis of late flowering mutants and ecotypes in Arabidopsis has revealed that such mechanisms are based upon several genetic pathways which may contain 80 or more. Together these loci co-ordinate flowering time with environmental variables (e.g. day-length, temperature, light quality, and nutrient availability) and with the developmental stage of the plant.

[0005] We have discovered transcription factors that regulate flowering phenotypes, and in particular that regulate timing of the onset of reproductive development, the duration of the phase in which floral meristems are initiated, or the duration of time for which floral organs persist prior to their abscission, or the number of flowers generated on a plant. These transcription factors therefore are useful to manipulate flowering phenotypes of a plant.

SUMMARY OF THE INVENTION

[0006] In a first aspect, the invention relates to a recombinant polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a nucleotide sequence encoding a polypeptide comprising a sequence selected from SEQ ID Nos. 2N, where N=1-12, or a complementary nucleotide sequence thereof; (b) a nucleotide sequence encoding a polypeptide comprising a conservatively substituted variant of a polypeptide of (a); (c) a nucleotide sequence comprising a sequence selected from those of SEQ ID Nos. 2N-1, where N=1-12, or a complementary nucleotide sequence thereof; (d) a nucleotide sequence comprising silent substitutions in a nucleotide sequence of (c); (e) a nucleotide sequence which hybridizes under stringent conditions over substantially the entire length of a nucleotide sequence of one or more of: (a), (b), (c), or (d); (f) a nucleotide sequence comprising at least 15 consecutive nucleotides of a sequence of any of (a)-(e); (g) a nucleotide sequence comprising a subsequence or fragment of any of (a)-(f), which subsequence or fragment encodes a polypeptide having a biological activity that modifies a plant's flowering phenotype; (h) a nucleotide sequence having at least 40% sequence identity to a nucleotide sequence of any of (a)-(g); (i) a nucleotide sequence having at least 85% sequence identity to a nucleotide sequence of any of (a)-(g); (j) a nucleotide sequence which encodes a polypeptide having at least 40% sequence identity to a polypeptide of SEQ ID Nos. 2N, where N=1-12; (k) a nucleotide sequence which encodes a polypeptide having at least 85% identity sequence identity to a polypeptide of SEQ ID Nos. 2N, where N=1-12; and (1) a nucleotide sequence which encodes a conserved domain of a polypeptide having at least 65% sequence identity to a conserved domain of a polypeptide of SEQ ID Nos. 2N, where N=1-12. The recombinant polynucleotide may further comprise a constitutive, inducible, or tissue-active promoter operably linked to the nucleotide sequence. The invention also relates to compositions comprising at least two of the above described polynucleotides.

[0007] In a second aspect, the invention is an isolated or recombinant polypeptide comprising a subsequence of at least about 15 contiguous amino acids encoded by the recombinant or isolated polynucleotide described above. These polynucleotides and polypeptides are useful for modifying the flowering phenotypes of a plant, and in particular for modifying timing of the onset of reproductive development, the duration of the phase in which floral meristems are initiated, or the duration of time for which floral organs persist prior to their abscission, or the number of flowers generated on a plant.

[0008] In another aspect, the invention is a transgenic plant comprising one or more of the above described recombinant polynucleotides. In yet another aspect, the invention is a plant with altered expression levels of a polynucleotide described above or a plant with altered expression or activity levels of an above described polypeptide. In a further aspect, the invention relates to a cloning or expression vector comprising the isolated or recombinant polynucleotide described above or cells comprising the cloning or expression vector.

[0009] In yet a further aspect, the invention relates to a composition produced by incubating a polynucleotide of the invention with a nuclease, a restriction enzyme, a polymerase; a polymerase and a primer; a cloning vector, or with a cell.

[0010] Furthermore, the invention relates to a method for producing a plant having a modified flowering phenotype, such as flowering time or flowering period. The method comprises altering the expression of an isolated or recombinant polynucleotide of the invention or altering the expression or activity of a polypeptide of the invention in a plant to produce a modified plant, and selecting the modified plant for a modified flowering time or flowering period phenotype.

[0011] In another aspect, the invention relates to a method of identifying a factor that is modulated by or interacts with a polypeptide encoded by a polynucleotide of the invention. The method comprises expressing a polypeptide encoded by the polynucleotide in a plant; and identifying at least one factor that is modulated by or interacts with the polypeptide. In one embodiment the method for identifying modulating or interacting factors is by detecting binding by the polypeptide to a promoter sequence, or by detecting interactions between an additional protein and the polypeptide in a yeast two hybrid system., or by detecting expression of a factor by hybridization to a microarray, subtractive hybridization or differential display.

[0012] In yet another aspect, the invention is a method of identifying a molecule that modulates activity or expression of a polynucleotide or polypeptide of interest. The method comprises placing the molecule in contact with a plant comprising the polynucleotide or polypeptide encoded by the polynucleotide of the invention and monitoring one or more of the expression level of the polynucleotide in the plant, the expression level of the polypeptide in the plant, and modulation of an activity of the polypeptide in the plant.

[0013] In yet another aspect, the invention relates to an integrated system, computer or computer readable medium comprising one or more character strings corresponding to a polynucleotide of the invention, or to a polypeptide encoded by the polynucleotide. The integrated system, computer or computer readable medium may comprise a link between one or more sequence strings to a modified plant flowering phenotype.

[0014] In yet another aspect, the invention is a method for identifying a sequence similar or homologous to one or more polynucleotides of the invention, or one or more polypeptides encoded by the polynucleotides. The method comprises providing a sequence database; and, querying the sequence database with one or more target sequences corresponding to the one or more polynucleotides or to the one or more polypeptides to identify one or more sequence members of the database that display sequence similarity or homology to one or more of the one or more target sequences.

[0015] The method may further comprise of linking the one or more of the polynucleotides of the invention, or encoded polypeptides, to a modified plant flowering phenotype.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING

[0016] The Sequence Listing provides exemplary polynucleotide and polypeptide sequences of the invention. These sequences may be employed to modify the flowering time or the flowering period of a plant.

DETAILED DESCRIPTION

[0017] The present invention relates to polynucleotides and polypeptides, e.g. for modifying phenotypes of plants.

[0018] In particular, the polynucleotides or polypeptides are useful for modifying traits associated with a plant's flowering time or flowering period when the expression levels of the polynucleotides or expression levels or activity levels of the polypeptides are altered compared with those found in a wild type plant. The flowering time of plants can be either decreased, increased or made inducible under specific conditions using the polynucleotides or polypeptides of this invention. These polynucleotides and polypeptides are also useful for modifying the duration of the phase in which floral meristems are initiated, or the duration of time for which floral organs persist prior to their abscission, or the number of flowers generated on a plant. Additionally, the polynucleotides and polypeptides are useful for modifying traits associated with modified vernalization requirements or flowering time characteristics, such as changes in flowering time in response to day-length, in response to temperature, in response to light quality, nutrient availability, and development stage of the plant, the length of flowering time which delays senescence and the like.

[0019] The polynucleotides of the invention encode plant transcription factors. The plant transcription factors are derived, e.g., from Arabidopsis thaliana and can belong, e.g., to one or more of the following transcription factor families: the AP2 (APETALA2) domain transcription factor family (Riechmann and Meyerowitz (1998) J. Biol. Chem. 379:633-646); the MYB transcription factor family (Martin and Paz-Ares (1997) Trends Genet. 13:67-73); the MADS domain transcription factor family (Riechmann and Meyerowitz (1997) J. Biol. Chem. 378:1079-1101); the WRKY protein family (Ishiguro and Nakamura (1994) Mol. Gen. Genet. 244:563-571); the ankyrin-repeat protein family (Zhang et al. (1992) Plant Cell 4:1575-1588); the miscellaneous protein (MISC) family (Kim et al. (1997) Plant J. 11:1237-1251); the zinc finger protein (Z) family (Klug and Schwabe (1995) FASEB J. 9: 597-604); the homeobox (HB) protein family (Duboule (1994) Guidebook to the Homeobox Genes, Oxford University Press); the CAAT-element binding proteins (Forsburg and Guarente (1989) Genes Dev. 3:1166-1178); the squamosa promoter binding proteins (SPB) (Klein et al. (1996) Mol. Gen. Genet. 1996 250:7-16); the NAM protein family; the IAA/AUX proteins (Rouse et al. (1998) Science 279:1371-1373); the HLH/MYC protein family (Littlewood et al. (1994) Prot. Profile 1:639-709); the DNA-binding protein (DBP) family (Tucker et al. (1994) EMBO J. 13:2994-3002); the bZIP family of transcription factors (Foster et al. (1994) FASEB J. 8:192-200); the BPF-1 protein (Box P-binding factor) family (da Costa e Silva et al. (1993) Plant J. 4:125-135); and the golden protein (GLD) family (Hall et al. (1998) Plant Cell 10:925-936). Exemplary transcription factors of the present invention are listed in the Sequence Listing.

[0020] In addition to methods for modifying a plant phenotype by employing one or more polynucleotides and polypeptides of the invention described herein, the polynucleotides and polypeptides of the invention have a variety of additional uses. These uses include their use in the recombinant production (i.e, expression) of proteins; as regulators of plant gene expression, as diagnostic probes for the presence of complementary or partially complementary nucleic acids (including for detection of natural coding nucleic acids); as substrates for further reactions, e.g., mutation reactions, PCR reactions, or the like, of as substrates for cloning e.g., including digestion or ligation reactions, and for identifying exogenous or endogenous modulators of the transcription factors.

DEFINITIONS

[0021] A “polynucleotide” is a nucleic acid sequence comprising a plurality of polymerized nucleotide residues, e.g., at least about 15 consecutive polymerized nucleotide residues, optionally at least about 30 consecutive nucleotides, at least about 50 consecutive nucleotides. In many instances, a polynucleotide comprises a nucleotide sequence encoding a polypeptide (or protein) or a domain or fragment thereof. Additionally, the polynucleotide may comprise a promoter, an intron, an enhancer region, a polyadenylation site, a translation initiation site, 5′ or 3′ untranslated regions, a reporter gene, a selectable marker, or the like. The polynucleotide can be single stranded or double stranded DNA or RNA. The polynucleotide optionally comprises modified bases or a modified backbone. The polynucleotide can be, e.g., genomic DNA or RNA, a transcript (such as an MRNA), a cDNA, a PCR product, a cloned DNA, a synthetic DNA or RNA, or the like. The polynucleotide can comprise a sequence in either sense or antisense orientations.

[0022] A “recombinant polynucleotide” is a polynucleotide that is not in its native state, e.g., the polynucleotide comprises a nucleotide sequence not found in nature, or the polynucleotide is in a context other than that in which it is naturally found, e.g., separated from nucleotide sequences with which it typically is in proximity in nature, or adjacent (or contiguous with) nucleotide sequences with which it typically is not in proximity. For example, the sequence at issue can be cloned into a vector, or otherwise recombined with one or more additional nucleic acid.

[0023] An “isolated polynucleotide” is a polynucleotide whether naturally occurring or recombinant, that is present outside the cell in which it is typically found in nature, whether purified or not. Optionally, an isolated polynucleotide is subject to one or more enrichment or purification procedures, e.g., cell lysis, extraction, centrifugation, precipitation, or the like.

[0024] A “recombinant polypeptide” is a polypeptide produced by translation of a recombinant polynucleotide. An “isolated polypeptide,” whether a naturally occurring or a recombinant polypeptide, is more enriched in (or out of) a cell than the polypeptide in its natural state in a wild type cell, e.g., more than about 5% enriched, more than about 10% enriched, or more than about 20%, or more than about 50%, or more, enriched, i.e., alternatively denoted: 105%, 110%, 120%, 150% or more, enriched relative to wild type standardized at 100%. Such an enrichment is not the result of a natural response of a wild type plant. Alternatively, or additionally, the isolated polypeptide is separated from other cellular components with which it is typically associated, e.g., by any of the various protein purification methods herein.

[0025] The term “transgenic plant” refers to a plant that contains genetic material, not found in a wild type plant of the same species, variety or cultivar. The genetic material may include a transgene, an insertional mutagenesis event (such as by transposon or T-DNA insertional mutagenesis), an activation tagging sequence, a mutated sequence, a homologous recombination event or a sequence modified by chimeraplasty. Typically, the foreign genetic material has been introduced into the plant by human manipulation.

[0026] A transgenic plant may contain an expression vector or cassette. The expression cassette typically comprises a polypeptide-encoding sequence operably linked (i.e., under regulatory control of) to appropriate inducible or constitutive regulatory sequences that allow for the expression of polypeptide. The expression cassette can be introduced into a plant by transformation or by breeding after transformation of a parent plant. A plant refers to a whole plant as well as to a plant part, such as seed, fruit, leaf, or root, plant tissue, plant cells or any other plant material, e.g., a plant explant, as well as to progeny thereof, and to in vitro systems that mimic biochemical or cellular components or processes in a cell.

[0027] The phrase “ectopically expression or altered expression” in reference to a polynucleotide indicates that the pattern of expression in, e.g., a transgenic plant or plant tissue, is different from the expression pattern in a wild type plant or a reference plant of the same species. For example, the polynucleotide or polypeptide is expressed in a cell or tissue type other than a cell or tissue type in which the sequence is expressed in the wild type plant, or by expression at a time other than at the time the sequence is expressed in the wild type plant, or by a response to different inducible agents, such as hormones or environmental signals, or at different expression levels (either higher or lower) compared with those found in a wild type plant. The term also refers to altered expression patterns that are produced by lowering the levels of expression to below the detection level or completely abolishing expression. The resulting expression pattern can be transient or stable, constitutive or inducible. In reference to a polypeptide, the term “ectopic expression or altered expression” further may relate to altered activity levels resulting from the interactions of the polypeptides with exogenous or endogenous modulators or from interactions with factors or as a result of the chemical modification of the polypeptides.

[0028] The term “fragment” or “domain,” with respect to a polypeptide, refers to a subsequence of the polypeptide. In some cases, the fragment or domain, is a subsequence of the polypeptide which performs at least one biological function of the intact polypeptide in substantially the same manner, or to a similar extent, as does the intact polypeptide. For example, a polypeptide fragment can comprise a recognizable structural motif or functional domain such as a DNA binding domain that binds to a DNA promoter region, an activation domain or a domain for protein-protein interactions. Fragments can vary in size from as few as 6 amino acids to the full length of the intact polypeptide, but are preferably at least about 30 amino acids in length and more preferably at least about 60 amino acids in length. In reference to a nucleotide sequence, “a fragment” refers to any subsequence of a polynucleotide, typically, of at least consecutive about 15 nucleotides, preferably at least about 30 nucleotides, more preferably at least about 50, of any of the sequences provided herein.

[0029] The term “trait” refers to a physiological, morphological, biochemical or physical characteristic of a plant or particular plant material or cell. In some instances, this characteristic is visible to the human eye, such as seed or plant size, or can be measured by available biochemical techniques, such as the protein, starch or oil content of seed or leaves or by the observation of the expression level of genes, e.g., by employing Northern analysis, RT-PCR, microarray gene expression assays or reporter gene expression systems, or by agricultural observations such as stress tolerance, yield or pathogen tolerance.

[0030] “Trait modification” refers to a detectable difference in a characteristic in a plant ectopically expressing a polynucleotide or polypeptide of the present invention relative to a plant not doing so, such as a wild type plant. In some cases, the trait modification can be evaluated quantitatively. For example, the trait modification can entail at least about a 2% increase or decrease in an observed trait (difference), at least a 5% difference, at least about a 10% difference, at least about a 20% difference, at least about a 30%, at least about a 50%, at least about a 70%, or at least about a 100%, or an even greater difference. It is known that there can be a natural variation in the modified trait. Therefore, the trait modification observed entails a change of the normal distribution of the trait in the plants compared with the distribution observed in wild type plant.

[0031] Trait modifications of particular interest include those to seed ( such as embryo or endosperm), fruit, root, flower, leaf, stem, shoot, seedling or the like, including: enhanced tolerance to environmental conditions including freezing, chilling, heat, drought, water saturation, radiation and ozone; improved tolerance to microbial, fungal or viral diseases; improved tolerance to pest infestations, including nematodes, mollicutes, parasitic higher plants or the like; decreased herbicide sensitivity; improved tolerance of heavy metals or enhanced ability to take up heavy metals; improved growth under poor photoconditions (e.g., low light and/or short day length), or changes in expression levels of genes of interest. Other phenotype that can be modified relate to the production of plant metabolites, such as variations in the production of taxol, tocopherol, tocotrienol, sterols, phytosterols, vitamins, wax monomers, anti-oxidants, amino acids, lignins, cellulose, tannins, prenyllipids (such as chlorophylls and carotenoids), glucosinolates, and terpenoids, enhanced or compositionally altered protein or oil production (especially in seeds), or modified sugar (insoluble or soluble) and/or starch composition. Physical plant characteristics that can be modified include cell development (such as the number of trichomes), fruit and seed size and number, yields of plant parts such as stems, leaves and roots, the stability of the seeds during storage, characteristics of the seed pod (e.g., susceptibility to shattering), root hair length and quantity, internode distances, or the quality of seed coat. Plant growth characteristics that can be modified include growth rate, germination rate of seeds, vigor of plants and seedlings, leaf and flower senescence, male sterility, apomixis, flowering time, flower abscission, rate of nitrogen uptake, biomass or transpiration characteristics, as well as plant architecture characteristics such as apical dominance, branching patterns, number of organs, organ identity, organ shape or size.

POLYPEPTIDES AND POLYNUCLEOTIDES OF THE INVENTION

[0032] The present invention provides, among other things, transcription factors (TFs), and transcription factor homologue polypeptides, and isolated or recombinant polynucleotides encoding the polypeptides. These polypeptides and polynucleotides may be employed to modify a plant's flowering phenotype.

[0033] Exemplary polynucleotides encoding the polypeptides of the invention were identified in the Arabidopsis thaliana GenBank database using publicly available sequence analysis programs and parameters. Sequences initially identified were then further characterized to identify sequences comprising specified sequence strings corresponding to sequence motifs present in families of known transcription factors. Polynucleotide sequences meeting such criteria were confirmed as transcription factors.

[0034] Additional polynucleotides of the invention were identified by screening Arabidopsis thaliana and/or other plant cDNA libraries with probes corresponding to known transcription factors under low stringency hybridization conditions. Additional sequences, including full length coding sequences were subsequently recovered by the rapid amplification of cDNA ends (RACE) procedure, using a commercially available kit according to the manufacturer's instructions. Where necessary, multiple rounds of RACE are performed to isolate 5′ and 3′ ends. The full length cDNA was then recovered by a routine end-to-end polymerase chain reaction (PCR) using primers specific to the isolated 5′ and 3′ ends. Exemplary sequences are provided in the Sequence Listing.

[0035] The polynucleotides of the invention were ectopically expressed in overexpressor or knockout plants and changes in the flowering phenotype of the plants was observed. Therefore, the polynucleotides and polypeptides can be employed to improve the flowering phenotype of plants.

Making polynucleotides

[0036] The polynucleotides of the invention include sequences that encode transcription factors and transcription factor homologue polypeptides and sequences complementary thereto, as well as unique fragments of coding sequence, or sequence complementary thereto. Such polynucleotides can be, e.g., DNA or RNA, e.g., mRNA, cRNA, synthetic RNA, genomic DNA, cDNA synthetic DNA, oligonucleotides, etc. The polynucleotides are either double-stranded or single-stranded, and include either, or both sense (i.e., coding) sequences and antisense (i.e., non-coding, complementary) sequences. The polynucleotides include the coding sequence of a transcription factor, or transcription factor homologue polypeptide, in isolation, in combination with additional coding sequences (e.g., a purification tag, a localization signal, as a fusion-protein, as a pre-protein, or the like), in combination with non-coding sequences (e.g., introns or inteins, regulatory elements such as promoters, enhancers, terminators, and the like), and/or in a vector or host environment in which the polynucleotide encoding a transcription factor or transcription factor homologue polypeptide is an endogenous or exogenous gene.

[0037] A variety of methods exist for producing the polynucleotides of the invention. Procedures for identifying and isolating DNA clones are well known to those of skill in the art, and are described in, e.g., Berger and Kimmel, Guide to Molecular Cloning Techniques Methods in Enzymology volume 152 Academic Press, Inc., San Diego, Calif. (“Berger”); Sambrook et al., Molecular Cloning—A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1989 (“Sambrook”) and Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (supplemented through 2000) (“Ausubel”).

[0038] Alternatively, polynucleotides of the invention, can be produced by a variety of in vitro amplification methods adapted to the present invention by appropriate selection of specific or degenerate primers. Examples of protocols sufficient to direct persons of skill through in vitro amplification methods, including the polymerase chain reaction (PCR) the ligase chain reaction (LCR), Qbeta-replicase amplification and other RNA polymerase mediated techniques (e.g., NASBA), e.g., for the production of the homologous nucleic acids of the invention are found in Berger, Sambrook, and Ausubel, as well as Mullis et al., (1987) PCR Protocols A Guide to Methods and Applications (Innis et al. eds) Academic Press Inc. San Diego, Calif. (1990) (Innis). Improved methods for cloning in vitro amplified nucleic acids are described in Wallace et al., U.S. Pat. No. 5,426,039. Improved methods for amplifying large nucleic acids by PCR are summarized in Cheng et al. (1994) Nature 369: 684-685 and the references cited therein, in which PCR amplicons of up to 40 kb are generated. One of skill will appreciate that essentially any RNA can be converted into a double stranded DNA suitable for restriction digestion, PCR expansion and sequencing using reverse transcriptase and a polymerase. See, e.g., Ausubel, Sambrook and Berger, all stipra.

[0039] Alternatively, polynucleotides and oligonucleotides of the invention can be assembled from fragments produced by solid-phase synthesis methods. Typically, fragments of up to approximately 100 bases are individually synthesized and then enzymatically or chemically ligated to produce a desired sequence, e.g., a polynucletotide encoding all or part of a transcription factor. For example, chemical synthesis using the phosphoramidite method is described, e.g., by Beaucage et al. (1981) Tetrahedron Letters 22:1859-69; and Matthes et al. (1984) EMBO J. 3:801-5. According to such methods, oligonucleotides are synthesized, purified, annealed to their complementary strand, ligated and then optionally cloned into suitable vectors. And if so desired, the polynucleotides and polypeptides of the invention can be custom ordered from any of a number of commercial suppliers.

HOMOLOGOUS SEQUENCES

[0040] Sequences homologous, i.e., that share significant sequence identity or similarity, to those provided in the Sequence Listing, derived from Arabidopsis thaliana or from other plants of choice are also an aspect of the invention. Homologous sequences can be derived from any plant including monocots and dicots and in particular agriculturally important plant species, including but not limited to, crops such as soybean, wheat, corn, potato, cotton, rice, oilseed rape (including canola), sunflower, alfalfa, sugarcane and turf, or fruits and vegetables, such as banana, blackberry, blueberry, strawberry, and raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers, pineapple, spinach, squash, sweet corn, tobacco, tomato, watermelon, rosaceous fruits (such as apple, peach, pear, cherry and plum) and vegetable brassicas (such as broccoli, cabbage, cauliflower, brussel sprouts and kohlrabi). Other crops, fruits and vegetables whose phenotype can be changed include barley, rye, millet, sorghum, currant, avocado, citrus fruits such as oranges, lemons, grapefruit and tangerines, artichoke, cherries, nuts such as the walnut and peanut, endive, leek, roots, such as arrowroot, beet, cassava, turnip, radish, yam, and sweet potato, and beans. The homologous sequences may also be derived from woody species, such pine, poplar and eucalyptus.

[0041] Transcription factors that are homologous to the listed sequences will typically share at least about 35% amino acid sequence identity. More closely related transcription factors can share at least about 50%, about 60%, about 65%, about 70%, about 75% or about 80% or about 90% or about 95% or about 98% or more sequence identity with the listed sequences. Factors that are most closely related to the listed sequences share, e.g., at least about 85%, about 90% or about 95% or more % sequence identity to the listed sequences. At the nucleotide level, the sequences will typically share at least about 40% nucleotide sequence identity, preferably at least about 50%, about 60%, about 70% or about 80% sequence identity, and more preferably about 85%, about 90%, about 95% or about 97% or more sequence identity to one or more of the listed sequences. The degeneracy of the genetic code enables major variations in the nucleotide sequence of a polynucleotide while maintaining the amino acid sequence of the encoded protein. Conserved domains within a transcription factor family may exhibit a higher degree of sequence homology, such as at least 65% sequence identity including conservative substitutions, and preferably at least 80% sequence identity. Exemplary conserved domains of the present invention include: for G2010 (SEQ ID Nos. 7 and 8) amino acid residues 54 through 127, for G1037 (SEQ ID Nos: 9 and 10) amino acid residues 11 through 134 or 200 through 248, for G1820 (SEQ ID Nos. 5 and 6) amino acid residues 41-159, for G11760 (SEQ ID Nos. 3 and 4) amino acid residues 2 through 57, and for G590 (SEQ ID Nos. 1 and 2) amino acid residues 193 through 253.

Identifying Nucleic Acids by Hybridization

[0042] Polynucleotides homologous to the sequences illustrated in the Sequence Listing can be identified, e.g., by hybridization to each other under stringent or under highly stringent conditions. Single stranded polynucleotides hybridize when they associate based on a variety of well characterized physico-chemical forces, such as hydrogen bonding, solvent exclusion, base stacking and the like. The stringency of a hybridization reflects the degree of sequence identity of the nucleic acids involved, such that the higher the stringency, the more similar are the two polynucleotide strands. Stringency is influenced by a variety of factors, including temperature, salt concentration and composition, organic and non-organic additives, solvents, etc. present in both the hybridization and wash solutions and incubations (and number), as described in more detail in the references cited above.

[0043] An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or northern blot is about 5° C. to 20° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Nucleic acid molecules that hybridize under stringent conditions will typically hybridize to a probe based on either the entire cDNA or selected portions, e.g., to a unique subsequence, of the cDNA under wash conditions of 0.2× SSC to 2.0× SSC, 0.1% SDS at 50-65° C., for example 0.2 × SSC, 0.1% SDS at 65° C. For identification of less closely related homologues washes can be performed at a lower temperature, e.g., 50° C. In general, stringency is increased by raising the wash temperature and/or decreasing the concentration of SSC.

[0044] As another example, stringent conditions can be selected such that an oligonucleotide that is perfectly complementary to the coding oligonucleotide hybridizes to the coding oligonucleotide with at least about a 5-1× higher signal to noise ratio than the ratio for hybridization of the perfectly complementary oligonucleotide to a nucleic acid encoding a transcription factor known as of the filing date of the application. Conditions can be selected such that a higher signal to noise ratio is observed in the particular assay which is used, e.g., about 15×, 25×, 35×, 50× or more. Accordingly, the subject nucleic acid hybridizes to the unique coding oligonucleotide with at least a 2× higher signal to noise ratio as compared to hybridization of the coding oligonucleotide to a nucleic acid encoding known polypeptide. Again, higher signal to noise ratios can be selected, e.g., about 5×, 10×, 25×, 35×, 50× or more. The particular signal will depend on the label used in the relevant assay, e.g., a fluorescent label, a colorimetric label, a radio active label, or the like.

[0045] Alternatively, transcription factor homologue polypeptides can be obtained by screening an expression library using antibodies specific for one or more transcription factors. With the provision herein of the disclosed transcription factor, and transcription factor homologue nucleic acid sequences, the encoded polypeptide(s) can be expressed and purified in a heterologous expression system (e.g., E. coli) and used to raise antibodies (monoclonal or polyclonal) specific for the polypeptide(s) in question. Antibodies can also be raised against synthetic peptides derived from transcription factor, or transcription factor homologue, amino acid sequences. Methods of raising antibodies are well known in the art and are described in Harlow and Lane (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York. Such antibodies can then be used to screen an expression library produced from the plant from which it is desired to clone additional transcription factor homologues, using the methods described above. The selected cDNAs can be confirmed by sequencing and enzymatic activity.

SEQUENCE VARIATIONS

[0046] It will readily be appreciated by those of skill in the art, that any of a variety of polynucleotide sequences are capable of encoding the transcription factors and transcription factor homologue polypeptides of the invention. Due to the degeneracy of the genetic code, many different polynucleotides can encode identical and/or substantially similar polypeptides in addition to those sequences illustrated in the Sequence Listing.

[0047] For example, Table I illustrates, e.g., that the codons AGC, AGT, TCA., TCC, TCG, and TCT all encode the same amino acid: serine. Accordingly, at each position in the sequence where there is a codon encoding serine, any of the above trinucleotide sequences can be used without altering the encoded polypeptide. TABLE 1 Amino acids Codon Alanine Ala A GCA GCC GCG GCU Cysteine Cys C TGC TGT Aspartic acid Asp D GAC GAT Glutamic acid Glu E GAA GAG Phenylalanine Phe F TTC TTT Glycine Gly G GGA GGC GGG GGT Histidine His H CAC CAT Isoleucine Ile I ATA ATC ATT Lysine Lys K AAA AAG Leucine Leu L TTA TTG CTA CTC CTG CTT Methionine Met M ATG Asparagine Asn N AAC AAT Proline Pro P CCA CCC CCG CCT Glutamine Gln Q CAA CAG Arginine Arg R AGA AGG CGA CGC CGG CGT Serine Ser S AGC AGT TCA TCC TCG TCT Threonine Thr T ACA ACC AGG ACT Valine Val V GTA GTC GTG GTT Tryptophan Trp W TGG Tyrosine Tyr Y TAC TAT

[0048] Sequence alterations that do not change the amino acid sequence encoded by the polynucleotide are termed “silent” variations. With the exception of the codons ATG and TGG, encoding methionine and tryptophan, respectively, any of the possible codons for the same amino acid can be substituted by a variety of techniques, e.g., site-directed mutagenesis, available in the art. Accordingly, any and all such variations of a sequence selected from the above table are a feature of the invention.

[0049] In addition to silent variations, other conservative variations that alter one, or a few amino acids in the encoded polypeptide, can be made without altering the function of the polypeptide, these conservative variants are, likewise, a feature of the invention.

[0050] For example, substitutions, deletions and insertions introduced into the sequences provided in the Sequence Listing are also envisioned by the invention. Such sequence modifications can be engineered into a sequence by site-directed mutagenesis (Wu (ed.) Meth. Enzymol. (1993) vol.217, Academic Press) or the other methods noted below. Amino acid substitutions are typically of single residues; insertions usually will be on the order of about from 1 to 10 amino acid residues; and deletions will range about from 1 to 30 residues. In preferred embodiments, deletions or insertions are made in adjacent pairs, e.g., a deletion of two residues or insertion of two residues. Substitutions, deletions, insertions or any combination thereof can be combined to arrive at a sequence. The mutations that are made in the polynucleotide encoding the transcription factor should not place the sequence out of reading frame and should not create complementary regions that could produce secondary MRNA structure. Preferably, the polypeptide encoded by the DNA performs the desired function.

[0051] Conservative substitutions are those in which at least one residue in the amino acid sequence has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the Table 2 when it is desired to maintain the activity of the protein. Table 2 shows amino acids which can be substituted for an amino acid in a protein and which are typically regarded as conservative substitutions. TABLE 2 Residue Conservative Substitutions Ala Ser Arg Lys Asn Gln; His Asp Glu Gln Asn Cys Ser Glu Asp Gly Pro His Asn; Gln Ile Leu, Val Leu Ile; Val Lys Arg; Gln Met Leu; Ile Phe Met; Leu; Tyr Ser Thr; Gly Thr Ser; Val Trp Tyr Tyr Trp; Phe Val Ile; Leu

[0052] Substitutions that are less conservative than those in Table 2 can be selected by picking residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. The substitutions which in general are expected to produce the greatest changes in protein properties will be those in which (a) a hydrophilic residue, e.g., seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g., leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine.

FURTHER MODIFYING SEQUENCES OF THE INVENTION—MUTATION/FORCED EVOLUTION

[0053] In addition to generating silent or conservative substitutions as noted, above, the present invention optionally includes methods of modifying the sequences of the Sequence Listing. In the methods, nucleic acid or protein modification methods are used to alter the given sequences to produce new sequences and/or to chemically or enzymatically modify given sequences to change the properties of the nucleic acids or proteins.

[0054] Thus, in one embodiment, given nucleic acid sequences are modified, e.g., according to standard mutagenesis or artificial evolution methods to produce modified sequences. For example, Ausubel, supra, provides additional details on mutagenesis methods. Artificial forced evolution methods are described, e.g., by Stemmer (1994) Nature 370:389-391, and Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751. Many other mutation and evolution methods are also available and expected to be within the skill of the practitioner.

[0055] Similarly, chemical or enzymatic alteration of expressed nucleic acids and polypeptides can be performed by standard methods. For example, sequence can be modified by addition of lipids, sugars, peptides, organic or inorganic compounds, by the inclusion of modified nucleotides or amino acids, or the like. For example, protein modification techniques are illustrated in Ausubel, supra. Further details on chemical and enzymatic modifications can be found herein. These modification methods can be used to modify any given sequence, or to modify any sequence produced by the various mutation and artificial evolution modification methods noted herein.

[0056] Accordingly, the invention provides for modification of any given nucleic acid by mutation, evolution, chemical or enzymatic modification, or other available methods, as well as for the products produced by practicing such methods, e.g., using the sequences herein as a starting substrate for the various modification approaches.

[0057] For example, optimized coding sequence containing codons preferred by a particular prokaryotic or eukaryotic host can be used e.g., to increase the rate of translation or to produce recombinant RNA transcripts having desirable properties, such as a longer half-life, as compared with transcripts produced using a non-optimized sequence. Translation stop codons can also be modified to reflect host preference. For example, preferred stop codons for S. cerevisiae and mammals are TAA and TGA, respectively. The preferred stop codon for monocotyledonous plants is TGA, whereas insects and E. coli prefer to use TAA as the stop codon.

[0058] The polynucleotide sequences of the present invention can also be engineered in order to alter a coding sequence for a variety of reasons, including but not limited to, alterations which modify the sequence to facilitate cloning, processing and/or expression of the gene product. For example, alterations are optionally introduced using techniques which are well known in the art, e.g., site-directed mutagenesis, to insert new restriction sites, to alter glycosylation patterns, to change codon preference, to introduce splice sites, etc.

[0059] Furthermore, a fragment or domain derived from any of the polypeptides of the invention can be combined with domains derived from other transcription factors or synthetic domains to modify the biological activity of a transcription factor. For instance, a DNA binding domain derived from a transcription factor of the invention can be combined with the activation domain of another transcription factor or with a synthetic activation domain. A transcription activation domain assists in initiating transcription from a DNA binding site. Examples include the transcription activation region of VP16 or GAL4 (Moore et al. (1998) Proc. Natl. Acad. Sci. USA 95: 376-381; and Aoyama et al. (1995) Plant Cell 7:1773-1785), peptides derived from bacterial sequences (Ma and Ptashne (1987) Cell 51; 113-119) and synthetic peptides (Giniger and Ptashne, (1987) Nature 330:670-672).

EXPRESSION AND MODIFICATION OF POLYPEPTIDES

[0060] Typically, polynucleotide sequences of the invention are incorporated into recombinant DNA (or RNA) molecules that direct expression of polypeptides of the invention in appropriate host cells, transgenic plants, in vitro translation systems, or the like. Due to the inherent degeneracy of the genetic code, nucleic acid sequences which encode substantially the same or a functionally equivalent amino acid sequence can be substituted for any listed sequence to provide for cloning and expressing the relevant homologue.

Vectors, Promoters and Expression Systems

[0061] The present invention includes recombinant constructs comprising one or more of the nucleic acid sequences herein. The constructs typically comprise a vector, such as a plasmid, a cosmid, a phage, a virus (e.g., a plant virus), a bacterial artificial chromosome (BAC), a yeast artificial chromosome (YAC), or the like, into which a nucleic acid sequence of the invention has been inserted, in a forward or reverse orientation. In a preferred aspect of this embodiment, the construct further comprises regulatory sequences, including, for example, a promoter, operably linked to the sequence. Large numbers of suitable vectors and promoters are known to those of skill in the art, and are commercially available.

[0062] General texts which describe molecular biological techniques useful herein, including the use and production of vectors, promoters and many other relevant topics, include Berger, Sambrook and Ausubel, supra. Any of the identified sequences can be incorporated into a cassette or vector, e.g., for expression in plants. A number of expression vectors suitable for stable transformation of plant cells or for the establishment of transgenic plants have been described including those described in Weissbach and Weissbach, (1989) Methods for Plant Molecular Biology, Academic Press, and Gelvin et al., (1990) Plant Molecular Biology Manual, Kluwer Academic Publishers. Specific examples include those derived from a Ti plasmid of Agrobacterium tumefaciens, as well as those disclosed by Herrera-Estrella et al. (1983) Nature 303: 209, Bevan (1984) Nucl Acid Res. 12: 8711-8721, Klee (1985) Bio/Technology 3: 637-642, for dicotyledonous plants.

[0063] Alternatively, non-Ti vectors can be used to transfer the DNA into monocotyledonous plants and cells by using free DNA delivery techniques. Such methods can involve, for example, the use of liposomes, electroporation, microprojectile bombardment, silicon carbide whiskers, and viruses. By using these methods transgenic plants such as wheat, rice (Christou (1991) Bio/Technology 9: 957-962) and corn (Gordon-Kamm (1990) Plant Cell 2: 603-618) can be produced. An immature embryo can also be a good target tissue for monocots for direct DNA delivery techniques by using the particle gun (Weeks et al. (1993) Plant Physiol 102: 1077-1084; Vasil (1993) Bio/Technology 10: 667-674; Wan and Lemeaux (1994) Plant Physiol 104: 37-48, and for Agrobacterium-mediated DNA transfer (Ishida et al. (1996) Nature Biotech 14: 745-750).

[0064] Typically, plant transformation vectors include one or more cloned plant coding sequence (genomic or cDNA) under the transcriptional control of 5′ and 3′ regulatory sequences and a dominant selectable marker. Such plant transformation vectors typically also contain a promoter (e.g., a regulatory region controlling inducible or constitutive, environmentally-or developmentally-regulated, or cell- or tissue-specific expression), a transcription initiation start site, an RNA processing signal (such as intron splice sites), a transcription termination site, and/or a polyadenylation signal.

[0065] Examples of constitutive plant promoters which can be useful for expressing the TF sequence include: the cauliflower mosaic virus (CaMV) 35S promoter, which confers constitutive, high-level expression in most plant tissues (see, e.g., Odel et al. (1985) Nature 313:810); the nopaline synthase promoter (An et al. (1988) Plant Physiol 88:547); and the octopine synthase promoter (Fromm et al. (1989) Plant Cell 1: 977).

[0066] A variety of plant gene promoters that regulate gene expression in response to environmental, hormonal, chemical, developmental signals, and in a tissue-active manner can be used for expression of a TF sequence in plants. Choice of a promoter is based largely on the phenotype of interest and is determined by such factors as tissue (e.g., seed, fruit, root, pollen, vascular tissue, flower, carpel, etc.), inducibility (e.g., in response to wounding, heat, cold, drought, light, pathogens, etc.), timing, developmental stage, and the like. Numerous known promoters have been characterized and can favorable be employed to promote expression of a polynucleotide of the invention in a transgenic plant or cell of interest. For example, tissue specific promoters include: seed-specific promoters (such as the napin, phaseolin or DC3 promoter described in U.S. Pat. No. 5,773,697), fruit-specific promoters that are active during fruit ripening (such as the dru 1 promoter (U.S. Pat. No. 5,783,393), or the 2A11 promoter (U.S. Pat. No. 4,943,674) and the tomato polygalacturonase promoter (Bird et al. (1988) Plant Mol Biol 11:651), root-specific promoters, such as those disclosed in U.S. Pat. Nos. 5,618,988, 5,837,848 and 5,905,186, pollen-active promoters such as PTA29, PTA26 and PTA13 (U.S. Pat. No. 5,792,929), promoters active in vascular tissue (Ringli and Keller (1998) Plant Mol Biol 37:977-988), flower-specific (Kaiser et al, (1995) Plant Mol Biol 28:231-243), pollen (Baerson et al. (1994) Plant Mol Biol 26:1947-1959), carpels (Ohl et al. (1990) Plant Cell 2:837-848), pollen and ovules (Baerson et al. (1993) Plant Mol Biol 22:255-267), auxin-inducible promoters (such as that described in van der Kop et al. (1999) Plant Mol Biol 39:979-990 or Baumann et al. (1999) Plant Cell 11:323-334), cytokinin-inducible promoter (Guevara-Garcia (1998) Plant Mol Biol 38:743-753), promoters responsive to gibberellin (Shi et al. (1998) Plant Mol Biol 38:1053-1060, Willmott et al. (1998) 38:817-825) and the like. Additional promoters are those that elicit expression in response to heat (Ainley et al. (1993) Plant Mol Biol 22: 13-23), light (e.g., the pea rbcS-3A promoter, Kuhlemeier et al. (1989) Plant Cell 1:471, and the maize rbcS promoter, Schaffner and Sheen (1991) Plant Cell 3: 997); wounding (e.g., wunI, Siebertz et al. (1989) Plant Cell 1: 961); pathogens (such as the PR-1 promoter described in Buchel et al. (1999) Plant Mol. Biol. 40:387-396, and the PDF1.2 promoter described in Manners et al. (1998) Plant Mol. Biol. 38:1071-80), and chemicals such as methyl jasmonate or salicylic acid (Gatz et al. (1997) Plant Mol Biol 48: 89-108). In addition, the timing of the expression can be controlled by using promoters such as those acting at senescence (An and Amazon (1995) Science 270: 1986-1988); or late seed development (Odell et al. (1994) Plant Physiol 106:447458).

[0067] Plant expression vectors can also include RNA processing signals that can be positioned within, upstream or downstream of the coding sequence. In addition, the expression vectors can include additional regulatory sequences from the 3′-untranslated region of plant genes, e.g., a 3′ terminator region to increase MRNA stability of the mRNA, such as the PI-II terminator region of potato or the octopine or nopaline synthase 3′ terminator regions.

Additional Expression Elements

[0068] Specific initiation signals can aid in efficient translation of coding sequences.

[0069] These signals can include, e.g., the ATG initiation codon and adjacent sequences. In cases where a coding sequence, its initiation codon and upstream sequences are inserted into the appropriate expression vector, no additional translational control signals may be needed. However, in cases where only coding sequence (e.g., a mature protein coding sequence), or a portion thereof, is inserted, exogenous transcriptional control signals including the ATG initiation codon can be separately provided. The initiation codon is provided in the correct reading frame to facilitate transcription. Exogenous transcriptional elements and initiation codons can be of various origins, both natural and synthetic. The efficiency of expression can be enhanced by the inclusion of enhancers appropriate to the cell system in use.

Exression Hosts

[0070] The present invention also relates to host cells which are transduced with vectors of the invention, and the production of polypeptides of the invention (including fragments thereof) by recombinant techniques. Host cells are genetically engineered (i.e, nucleic acids are introduced, e.g., transduced, transformed or transfected) with the vectors of this invention, which may be, for example, a cloning vector or an expression vector comprising the relevant nucleic acids herein. The vector is optionally a plasmid, a viral particle, a phage, a naked nucleic acids, etc. The engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants, or amplifying the relevant gene. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to those skilled in the art and in the references cited herein, including, Sambrook and Ausubel.

[0071] The host cell can be a eukaryotic cell, such as a yeast cell, or a plant cell, or the host cell can be a prokaryotic cell, such as a bacterial cell. Plant protoplasts are also suitable for some applications. For example, the DNA fragments are introduced into plant tissues, cultured plant cells or plant protoplasts by standard methods including electroporation (Fromm et al., (1985) Proc. Natl. Acad. Sci. U.S.A 82, 5824, infection by viral vectors such as cauliflower mosaic virus (CaMV) (Hohn et al., (1982) Molecular Biology of Plant Tumors, (Academic Press, New York) pp. 549-560; U.S. Pat. No. 4,407,956), high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface (Klein et al., (1987) Nature 327, 70-73), use of pollen as vector (WO 85/01856), or use of Agrobacterium tumefaciens or A. rhizogenes carrying a T-DNA plasmid in which DNA fragments are cloned. The T-DNA plasmid is transmitted to plant cells upon infection by Agrobacterium tumefaciens, and a portion is stably integrated into the plant genome (Horsch et al. (1984) Science 233:496-498; Fraley et al. (1983) Proc. Natl. Acad. Sci. U.S.A 80, 4803).

[0072] The cell can include a nucleic acid of the invention which encodes a polypeptide, wherein the cells expresses a polypeptide of the invention. The cell can also include vector sequences, or the like. Furthermore, cells and transgenic plants which include any polypeptide or nucleic acid above or throughout this specification, e.g., produced by transduction of a vector of the invention, are an additional feature of the invention.

[0073] For long-term, high-yield production of recombinant proteins, stable expression can be used. Host cells transformed with a nucleotide sequence encoding a polypeptide of the invention are optionally cultured under conditions suitable for the expression and recovery of the encoded protein from cell culture. The protein or fragment thereof produced by a recombinant cell may be secreted, membrane-bound, or contained intracellularly, depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides encoding mature proteins of the invention can be designed with signal sequences which direct secretion of the mature polypeptides through a prokaryotic or eukaryotic cell membrane.

IDENTIFICATION OF ADDITIONAL FACTORS

[0074] A transcription factor provided by the present invention can also be used to identify additional endogenous or exogenous molecules that can affect a phentoype or trait of interest. On the one hand, such molecules include organic (small or large molecules) and/or inorganic compounds that affect expression of (i.e., regulate) a particular transcription factor. Alternatively, such molecules include endogenous molecules that are acted upon either at a transcriptional level by a transcription factor of the invention to modify a phenotype as desired. For example, the transcription factors can be employed to identify one or more downstream gene with which is subject to a regulatory effect of the transcription factor. In one approach, a transcription factor or transcription factor homologue of the invention is expressed in a host cell, e.g, a transgenic plant cell, tissue or explant, and expression products, either RNA or protein, of likely or random targets are monitored, e.g., by hybridization to a microarray of nucleic acid probes corresponding to genes expressed in a tissue or cell type of interest, by two-dimensional gel electrophoresis of protein products, or by any other method known in the art for assessing expression of gene products at the level of RNA or protein. Alternatively, a transcription factor of the invention can be used to identify promoter sequences (i.e., binding sites) involved in the regulation of a downstream target. After identifying a promoter sequence, interactions between the transcription factor and the promoter sequence can be modified by changing specific nucleotides in the promoter sequence or specific amino acids in the transcription factor that interact with the promoter sequence to alter a plant trait. Typically, transcription factor DNA binding sites are identified by gel shift assays. After identifying the promoter regions, the promoter region sequences can be employed in double-stranded DNA arrays to identify molecules that affect the interactions of the transcription factors with their promoters (Bulyk et al. (1999) Nature Biotechnology 17:573-577).

[0075] The identified transcription factors are also useful to identify proteins that modify the activity of the transcription factor. Such modification can occur by covalent modification, such as by phosphorylation, or by protein-protein (homo or-heteropolymer) interactions. Any method suitable for detecting protein-protein interactions can be employed. Among the methods that can be employed are co-immunoprecipitation, cross-linking and co-purification through gradients or chromatographic columns, and the two-hybrid yeast system.

[0076] The two-hybrid system detects protein interactions in vivo and is described in Chien, et al., (1991), Proc. Natl. Acad. Sci. U.S.A 88, 9578-9582 and is commercially available from Clontech (Palo Alto, Calif.). In such a system, plasmids are constructed that encode two hybrid proteins: one consists of the DNA-binding domain of a transcription activator protein fused to the TF polypeptide and the other consists of the transcription activator protein's activation domain fused to an unknown protein that is encoded by a cDNA that has been recombined into the plasmid as part of a cDNA library. The DNA-binding domain fusion plasmid and the cDNA library are transformed into a strain of the yeast Saccharomyces cerevisiae that contains a reporter gene (e.g., lacZ) whose regulatory region contains the transcription activator's binding site. Either hybrid protein alone cannot activate transcription of the reporter gene. Interaction of the two hybrid proteins reconstitutes the functional activator protein and results in expression of the reporter gene, which is detected by an assay for the reporter gene product. Then, the library plasmids responsible for reporter gene expression are isolated and sequenced to identify the proteins encoded by the library plasmids. After identifying proteins that interact with the transcription factors, assays for compounds that interfere with the TF protein-protein interactions can be preformed.

IDENTIFICATION OF MODULATORS

[0077] In addition to the intracellular molecules described above, extracellular molecules that alter activity or expression of a transcription factor, either directly or indirectly, can be identified. For example, the methods can entail first placing a candidate molecule in contact with a plant or plant cell. The molecule can be introduced by topical administration, such as spraying or soaking of a plant, and then the molecule's effect on the expression or activity of the TF polypeptide or the expression of the polynucleotide monitored. Changes in the expression of the TF polypeptide can be monitored by use of polyclonal or monoclonal antibodies, gel electrophoresis or the like. Changes in the expression of the corresponding polynucleotide sequence can be detected by use of microarrays, Northerns, quantitative PCR, or any other technique for monitoring changes in mRNA expression. These techniques are exemplified in Ausubel et al. (eds) Current Protocols in Molecular Biology, John Wiley & Sons (1998). Such changes in the expression levels can be correlated with modified plant traits and thus identified molecules can be useful for soaking or spraying on fruit, vegetable and grain crops to modify traits in plants.

[0078] Essentially any available composition can be tested for modulatory activity of expression or activity of any nucleic acid or polypeptide herein. Thus, available libraries of compounds such as chemicals, polypeptides, nucleic acids and the like can be tested for modulatory activity. Often, potential modulator compounds can be dissolved in aqueous or organic (e.g., DMSO-based) solutions for easy delivery to the cell or plant of interest in which the activity of the modulator is to be tested. Optionally, the assays are designed to screen large modulator composition libraries by automating the assay steps and providing compounds from any convenient source to assays, which are typically run in parallel (e.g., in microtiter formats on microtiter plates in robotic assays).

[0079] In one embodiment, high throughput screening methods involve providing a combinatorial library containing a large number of potential compounds (potential modulator compounds). Such “combinatorial chemical libraries” are then screened in one or more assays, as described herein, to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as target compounds.

[0080] A combinatorial chemical library can be, e.g., a collection of diverse chemical compounds generated by chemical synthesis or biological synthesis. For example, a combinatorial chemical library such as a polypeptide library is formed by combining a set of chemical building blocks (e.g., in one example, amino acids) in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound of a set length). Exemplary libraries include peptide libraries, nucleic acid libraries, antibody libraries (see, e.g., Vaughn et al. (1996) Nature Biotechnology, 14(3):309-314 and PCT/U.S.96/10287), carbohydrate libraries (see, e.g., Liang et al. Science (1996) 274:1520-1522 and U.S. Pat. No. 5,593,853), peptide nucleic acid libraries (see, e.g., U.S. Pat. No. 5,539,083), and small organic molecule libraries (see, e.g., benzodiazepines, Baum C&EN Jan 18, page 33 (1993); isoprenoids, U.S. Pat. No. 5,569,588; thiazolidinones and metathiazanones, U.S. Pat. No. 5,549,974; pyrrolidines, U.S. Pat. Nos. 5,525,735 and 5,519,134; morpholino compounds, U.S. Pat. No. 5,506,337) and the like.

[0081] Preparation and screening of combinatorial or other libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Pat. No. 5,010,175, Furka, Int. J. Pept. Prot. Res. 37:487493 (1991) and Houghton et al. Nature 354:84-88 (1991)). Other chemistries for generating chemical diversity libraries can also be used.

[0082] In addition, as noted, compound screening equipment for high-throughput screening is generally available, e.g., using any of a number of well known robotic systems that have also been developed for solution phase chemistries useful in assay systems. These systems include automated workstations including an automated synthesis apparatus and robotic systems utilizing robotic arms. Any of the above devices are suitable for use with the present invention, e.g., for high-throughput screening of potential modulators. The nature and implementation of modifications to these devices (if any) so that they can operate as discussed herein will be apparent to persons skilled in the relevant art.

[0083] Indeed, entire high throughput screening systems are commercially available. These systems typically automate entire procedures including all sample and reagent pipetting, liquid dispensing, timed incubations, and final readings of the microplate in detector(s) appropriate for the assay. These configurable systems provide high throughput and rapid start up as well as a high degree of flexibility and customization. Similarly, microfluidic implementations of screening are also commercially available.

[0084] The manufacturers of such systems provide detailed protocols the various high throughput. Thus, for example, Zymark Corp. provides technical bulletins describing screening systems for detecting the modulation of gene transcription, ligand binding, and the like. The integrated systems herein, in addition to providing for sequence alignment and, optionally, synthesis of relevant nucleic acids, can include such screening apparatus to identify modulators that have an effect on one or more polynucleotides or polypeptides according to the present invention.

[0085] In some assays it is desirable to have positive controls to ensure that the components of the assays are working properly. At least two types of positive controls are appropriate. That is, known transcriptional activators or inhibitors can be incubated with cells/plants/ etc. in one sample of the assay, and the resulting increase/decrease in transcription can be detected by measuring the resulting increase in RNA/ protein expression, etc., according to the methods herein. It will be appreciated that modulators can also be combined with transcriptional activators or inhibitors to find modulators which inhibit transcriptional activation or transcriptional repression. Either expression of the nucleic acids and proteins herein or any additional nucleic acids or proteins activated by the nucleic acids or proteins herein, or both, can be monitored.

[0086] In an embodiment, the invention provides a method for identifying compositions that modulate the activity or expression of a polynucleotide or polypeptide of the invention. For example, a test compound, whether a small or large molecule, is placed in contact with a cell, plant (or plant tissue or explant), or composition comprising the polynucleotide or polypeptide of interest and a resulting effect on the cell, plant, (or tissue or explant) or composition is evaluated by monitoring, either directly or indirectly, one or more of: expression level of the polynucleotide or polypeptide, activity (or modulation of the activity) of the polynucleotide or polypeptide. In some cases, an alteration in a plant phenotype can be detected following contact of a plant (or plant cell, or tissue or explant) with the putative modulator, e.g., by modulation of expression or activity of a polynucleotide or polypeptide of the invention.

SUBSEQUENCES

[0087] Also contemplated are uses of polynucleotides, also referred to herein as oligonucleotides, typically having at least 12 bases, preferably at least 15, more preferably at least 20, 30, or 50 bases, which hybridize under at least highly stringent (or ultra-high stringent or ultra-ultra- high stringent conditions) conditions to a polynucleotide sequence described above. The polynucleotides may be used as probes, primers, sense and antisense agents, and the like, according to methods as noted supra.

[0088] Subsequences of the polynucleotides of the invention, including polynucleotide fragments and oligonucleotides are useful as nucleic acid probes and primers. An oligonucleotide suitable for use as a probe or primer is at least about 15 nucleotides in length, more often at least about 18 nucleotides, often at least about 21 nucleotides, frequently at least about 30 nucleotides, or about 40 nucleotides, or more in length. A nucleic acid probe is useful in hybridization protocols, e.g., to identify additional polypeptide homologues of the invention, including protocols for microarray experiments. Primers can be annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, and then extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR) or other nucleic-acid amplification methods. See Sambrook and Ausubel, supra.

[0089] In addition, the invention includes an isolated or recombinant polypeptide including a subsequence of at least about 15 contiguous amino acids encoded by the recombinant or isolated polynucleotides of the invention. For example, such polypeptides, or domains or fragments thereof, can be used as immunogens, e.g., to produce antibodies specific for the polypeptide sequence, or as probes for detecting a sequence of interest. A subsequence can range in size from about 15 amino acids in length up to and including the full length of the polypeptide.

PRODUCTION OF TRANSGENIC PLANTS

[0090] Modification of Traits

[0091] The polynucleotides of the invention are favorably employed to produce transgenic plants with various traits, or characteristics, that have been modified in a desirable manner, e.g., to improve the pathogen resistance of a plant. For example, alteration of expression levels or patterns (e.g., spatial or temporal expression patterns) of one or more of the transcription factors (or transcription factor homologues) of the invention, as compared with the levels of the same protein found in a wild type plant, can be used to modify a plant's traits. An illustrative example of trait modification, improved flowering phenotype, by altering expression levels of a particular transcription factor is described further in the Examples and the Sequence Listing.

[0092] Antisense and Cosuppression Approaches

[0093] In addition to expression of the nucleic acids of the invention as gene replacement or plant phenotype modification nucleic acids, the nucleic acids are also useful for sense and anti-sense suppression of expression, e.g., to down-regulate expression of a nucleic acid of the invention, e.g., as a further mechanism for modulating plant phenotype. That is, the nucleic acids of the invention, or subsequences or anti-sense sequences thereof, can be used to block expression of naturally occurring homologous nucleic acids. A variety of sense and anti-sense technologies are known in the art, e.g., as set forth in Lichtenstein and Nellen (1997) Antisense Technology: A Practical Approach IRL Press at Oxford University, Oxford, England. In general, sense or anti-sense sequences are introduced into a cell, where they are optionally amplified, e.g., by transcription. Such sequences include both simple oligonucleotide sequences and catalytic sequences such as ribozymes.

[0094] For example, a reduction or elimination of expression (i.e., a “knock-out”) of a transcription factor or transcription factor homologue polypeptide in a transgenic plant, e.g., to modify a plant trait, can be obtained by introducing an antisense construct corresponding to the polypeptide of interest as a cDNA. For antisense suppression, the transcription factor or homologue cDNA is arranged in reverse orientation (with respect to the coding sequence) relative to the promoter sequence in the expression vector. The introduced sequence need not be the full length cDNA or gene, and need not be identical to the cDNA or gene found in the plant type to be transformed. Typically, the antisense sequence need only be capable of hybridizing to the target gene or RNA of interest. Thus, where the introduced sequence is of shorter length, a higher degree of homology to the endogenous transcription factor sequence will be needed for effective antisense suppression. While antisense sequences of various lengths can be utilized, preferably, the introduced antisense sequence in the vector will be at least 30 nucleotides in length, and improved antisense suppression will typically be observed as the length of the antisense sequence increases. Preferably, the length of the antisense sequence in the vector will be greater than 100 nucleotides. Transcription of an antisense construct as described results in the production of RNA molecules that are the reverse complement of mRNA molecules transcribed from the endogenous transcription factor gene in the plant cell.

[0095] Suppression of endogenous transcription factor gene expression can also be achieved using a ribozyme. Ribozymes are RNA molecules that possess highly specific endoribonuclease activity. The production and use of ribozymes are disclosed in U.S. Pat. No. 4,987,071 and U.S. Pat. No. 5,543,508. Synthetic ribozyme sequences including antisense RNAs can be used to confer RNA cleaving activity on the antisense RNA, such that endogenous mRNA molecules that hybridize to the antisense RNA are cleaved, which in turn leads to an enhanced antisense inhibition of endogenous gene expression.

[0096] Vectors in which RNA encoded by a transcription factor or transcription factor homologue cDNA is over-expressed can also be used to obtain co-suppression of a corresponding endogenous gene, e.g., in the manner described in U.S. Pat. No. 5,231,020 to Jorgensen. Such co-suppression (also termed sense suppression) does not require that the entire transcription factor cDNA be introduced into the plant cells, nor does it require that the introduced sequence be exactly identical to the endogenous transcription factor gene of interest. However, as with antisense suppression, the suppressive efficiency will be enhanced as specificity of hybridization is increased, e.g., as the introduced sequence is lengthened, and/or as the sequence similarity between the introduced sequence and the endogenous transcription factor gene is increased.

[0097] Vectors expressing an untranslatable form of the transcription factor mRNA, e.g., sequences comprising one or more stop codon, or nonsense mutation) can also be used to suppress expression of an endogenous transcription factor, thereby reducing or eliminating it's activity and modifying one or more traits. Methods for producing such constructs are described in U.S. Pat. No. 5,583,021. Preferably, such constructs are made by introducing a premature stop codon into the transcription factor gene. Alternatively, a plant trait can be modified by gene silencing using double-strand RNA (Sharp (1999) Genes and Development 13: 139-141).

[0098] Another method for abolishing the expression of a gene is by insertion mutagenesis using the T-DNA of Agrobacterium tumefaciens. After generating the insertion mutants, the mutants can be screened to identify those containing the insertion in a transcription factor or transcription factor homologue gene. Plants containing a single transgene insertion event at the desired gene can be crossed to generate homozygous plants for the mutation (Koncz et al. (1992) Methods in Arabidopsis Research, World Scientific).

[0099] Alternatively, a plant phenotype can be altered by eliminating an endogenous gene, such as a transcription factor or transcription factor homologue, e.g., by homologous recombination (Kempin et al. (1997) Nature 389:802).

[0100] A plant trait can also be modified by using the cre-lox system (for example, as described in U.S. Pat. No.5,658,772). A plant genome can be modified to include first and second lox sites that are then contacted with a Cre recombinase. If the lox sites are in the same orientation, the intervening DNA sequence between the two sites is excised. If the lox sites are in the opposite orientation, the intervening sequence is inverted.

[0101] The polynucleotides and polypeptides of this invention can also be expressed in a plant in the absence of an expression cassette by manipulating the activity or expression level of the endogenous gene by other means. For example, by ectopically expressing a gene by T-DNA activation tagging (Ichikawa et al. (1997) Nature 390 698-701; Kakimoto et al. (1996) Science 274: 982-985). This method entails transforming a plant with a gene tag containing multiple transcriptional enhancers and once the tag has inserted into the genome, expression of a flanking gene coding sequence becomes deregulated. In another example, the transcriptional machinery in a plant can be modified so as to increase transcription levels of a polynucleotide of the invention (See, e.g., PCT Publications WO 96/06166 and WO 98/53057 which describe the modification of the DNA binding specificity of zinc finger proteins by changing particular amino acids in the DNA binding motif).

[0102] The transgenic plant can also include the machinery necessary for expressing or altering the activity of a polypeptide encoded by an endogenous gene, for example by altering the phosphorylation state of the polypeptide to maintain it in an activated state.

[0103] Transgenic plants (or plant cells, or plant explants, or plant tissues) incorporating the polynucleotides of the invention and/or expressing the polypeptides of the invention can be produced by a variety of well established techniques as described above. Following construction of a vector, most typically an expression cassette, including a polynucleotide, e.g., encoding a transcription factor or transcription factor homologue, of the invention, standard techniques can be used to introduce the polynucleotide into a plant, a plant cell, a plant explant or a plant tissue of interest. Optionally, the plant cell, explant or tissue can be regenerated to produce a transgenic plant.

[0104] The plant can be any higher plant, including gymnosperms, monocotyledonous and dicotyledenous plants. Suitable protocols are available for Leguminosae (alfalfa, soybean, clover, etc.), Umbelliferae (carrot, celery, parsnip), Cruciferae (cabbage, radish, rapeseed, broccoli, etc.), Curcurbitaceae (melons and cucumber), Gramineae (wheat, corn, rice, barley, millet, etc.), Solanaceae (potato, tomato, tobacco, peppers, etc.), and various other crops. See protocols described in Ammirato et al. (1984) Handbook of Plant Cell Culture—Crop Species. Macmillan Publ. Co. Shimamoto et al. (1989) Nature 338:274-276; Fromm et al. (1990) Bio/Technology 8:833-839; and Vasil et al. (1990) Bio/Technology 8:429-434.

[0105] Transformation and regeneration of both monocotyledonous and dicotyledonous plant cells is now routine, and the selection of the most appropriate transformation technique will be determined by the practitioner. The choice of method will vary with the type of plant to be transformed; those skilled in the art will recognize the suitability of particular methods for given plant types. Suitable methods can include, but are not limited to: electroporation of plant protoplasts; liposome-mediated transformation; polyethylene glycol (PEG) mediated transformation; transformation using viruses; micro-injection of plant cells; micro-projectile bombardment of plant cells; vacuum infiltration; and Agrobacterium tumeficiens mediated transformation. Transformation means introducing a nucleotide sequence in a plant in a manner to cause stable or transient expression of the sequence.

[0106] Successful examples of the modification of plant characteristics by transformation with cloned sequences which serve to illustrate the current knowledge in this field of technology, and which are herein incorporated by reference, include: U.S. Pat. Nos. 5,571,706; 5,677,175; 5,510,471; 5,750,386; 5,597,945; 5,589,615; 5,750,871; 5,268,526; 5,780,708; 5,538,880; 5,773,269; 5,736,369 and 5,610,042.

[0107] Following transformation, plants are preferably selected using a dominant selectable marker incorporated into the transformation vector. Typically, such a marker will confer antibiotic or herbicide resistance on the transformed plants, and selection of transformants can be accomplished by exposing the plants to appropriate concentrations of the antibiotic or herbicide.

[0108] After transformed plants are selected and grown to maturity, those plants showing a modified trait are identified. The modifed trait can be any of those traits described above. Additionally, to confirm that the modified trait is due to changes in expression levels or activity of the polypeptide or polynucleotide of the invention can be determined by analyzing mRNA expression using Northern blots, RT-PCR or microarrays, or protein expression using immunoblots or Western blots or gel shift assays.

INTEGRATED SYSTEMS—SEQUENCE IDENTITY

[0109] Additionally, the present invention may be an integrated system, computer or computer readable medium that comprises an instruction set for determining the identity of one or more sequences in a database. In addition, the instruction set can be used to generate or identify sequences that meet any specified criteria. Furthermore, the instruction set may be used to associate or link certain functional benefits, such improved flowering phenotype, with one or more identified sequence.

[0110] For example, the instruction set can include, e.g., a sequence comparison or other alignment program, e.g., an available program such as, for example, the Wisconsin Package Version 10.0, such as BLAST, FASTA, PILEUP, FINDPATTERNS or the like (GCG, Madision, Wisc.). Public sequence databases such as GenBank, EMBL, Swiss-Prot and PIR or private sequence databases such as PhytoSeq (Incyte Pharmaceuticals, Palo Alto, Calif.) can be searched.

[0111] Alignment of sequences for comparison can be conducted by the local homology algorithm of Smith and Waterman (1981) Adv. Appl. Math. 2:482, by the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. U.S.A. 85: 2444, by computerized implementations of these algorithms. After alignment, sequence comparisons between two (or more) polynucleotides or polypeptides are typically performed by comparing sequences of the two sequences over a comparison window to identify and compare local regions of sequence similarity. The comparison window can be a segment of at least about 20 contiguous positions, usually about 50 to about 200, more usually about 100 to about 150 contiguous positions. A description of the method is provided in Ausubel et al., supra.

[0112] A variety of methods of determining sequence relationships can be used, including manual alignment and computer assisted sequence alignment and analysis. This later approach is a preferred approach in the present invention, due to the increased throughput afforded by computer assisted methods. As noted above, a variety of computer programs for performing sequence alignment are available, or can be produced by one of skill.

[0113] One example algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm, which is described in Altschul et al. J. Mol. Biol 215:403410 (1990). Software for performing BLAST analyses is publicly available, e.g., through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always>0) and N (penalty score for mismatching residues; always<0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff (1989) Proc. Natl. Acad. Sci. U.S.A 89:10915).

[0114] In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul (1993) Proc. Natl. Acad. Sci. U.S.A 90:5873-5787). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence (and, therefore, in this context, homologous) if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, or less than about 0.01, and or even less than about 0.001. An additional example of a useful sequence alignment algorithm is PILEUP. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. The program can align, e.g., up to 300 sequences of a maximum length of 5,000 letters.

[0115] The integrated system, or computer typically includes a user input interface allowing a user to selectively view one or more sequence records corresponding to the one or more character strings, as well as an instruction set which aligns the one or more character strings with each other or with an additional character string to identify one or more region of sequence similarity. The system may include a link of one or more character strings with a particular phenotype or gene function. Typically, the system includes a user readable output element which displays an alignment produced by the alignment instruction set.

[0116] The methods of this invention can be implemented in a localized or distributed computing environment. In a distributed environment, the methods may implemented on a single computer comprising multiple processors or on a multiplicity of computers. The computers can be linked, e.g. through a common bus, but more preferably the computer(s) are nodes on a network. The network can be a generalized or a dedicated local or wide-area network and, in certain preferred embodiments, the computers may be components of an intra-net or an internet.

[0117] Thus, the invention provides methods for identifying a sequence similar or homologous to one or more polynucleotides as noted herein, or one or more target polypeptides encoded by the polynucleotides, or otherwise noted herein and may include linking or associating a given plant phenotype or gene function with a sequence. In the methods, a sequence database is provided (locally or across an inter or intra net) and a query is made against the sequence database using the relevant sequences herein and associated plant phenotypes or gene functions.

[0118] Any sequence herein can be entered into the database, before or after querying the database. This provides for both expansion of the database and, if done before the querying step, for insertion of control sequences into the database. The control sequences can be detected by the query to ensure the general integrity of both the database and the query. As noted, the query can be performed using a web browser based interface. For example, the database can be a centralized public database such as those noted herein, and the querying can be done from a remote terminal or computer across an internet or intranet.

EXAMPLES

[0119] The following examples are intended to illustrate but not limit the present invention.

EXAMPLE I FULL LENGTH GENE IDENTIFICATION AND CLONING

[0120] Putative transcription factor sequences (genomic or ESTs) related to known transcription factors were identified in the Arabidopsis thaliana GenBank database using the tblastn sequence analysis program using default parameters and a P-value cutoff threshold of −4 or −5 or lower, depending on the length of the query sequence. Putative transcription factor sequence hits were then screened to identify those containing particular sequence strings. If the sequence hits contained such sequence strings, the sequences were confirmed as transcription factors.

[0121] Alternatively, Arabidopsis thaliana cDNA libraries derived from different tissues or treatments, or genomic libraries were screened to identify novel members of a transcription family using a low stringency hybridization approach. Probes were synthesized using gene specific primers in a standard PCR reaction (annealing temperature 60° C.) and labeled with ³²P dCTP using the High Prime DNA Labeling Kit (Boehringer Mannheim). Purified radiolabelled probes were added to filters immersed in Church hybridization medium (0.5 M NaPO₄ pH 7.0, 7% SDS, 1 % w/v bovine serum albumin) and hybridized overnight at 60° C. with shaking. Filters were washed two times for 45 to 60 minutes with 1×SCC, 1% SDS at 60° C.

[0122] To identify additional sequence 5′ or 3′ of a partial cDNA sequence in a cDNA library, 5′ and 3′ rapid amplification of cDNA ends (RACE) was performed using the Marathon™ cDNA amplification kit (Clontech, Palo Alto, Calif.). Generally, the method entailed first isolating poly(A) MRNA, performing first and second strand cDNA synthesis to generate double stranded cDNA, blunting cDNA ends, followed by ligation of the Marathons Adaptor to the cDNA to form a library of adaptor-ligated ds cDNA.

[0123] Gene-specific primers were designed to be used along with adaptor specific primers for both 5′ and 3′ RACE reactions. Nested primers, rather than single primers, were used to increase PCR specificity. Using 5′ and 3′ RACE reactions, 5′ and 3′ RACE fragments were obtained, sequenced and cloned. The process can be repeated until 5′ and 3′ ends of the full-length gene were identified. Then the full-length cDNA was generated by PCR using primers specific to 5′ and 3′ ends of the gene by end-to-end PCR.

EXAMPLE II CONSTRUCTION OF EXPRESSION VECTORS

[0124] The sequence was amplified from a genomic or cDNA library using primers specific to sequences upstream and downstream of the coding region. The expression vector was pMEN20 or pMEN65, which are both derived from pMON3 16 (Sanders et al, (1987) Nucleic Acids Research 15:1543-58) and contain the CaMV 35S promoter to express transgenes. To clone the sequence into the vector, both pMEN20 and the amplified DNA fragment were digested separately with SalI and NotI restriction enzymes at 37° C. for 2 hours. The digestion products were subject to electrophoresis in a 0.8% agarose gel and visualized by ethidium bromide staining. The DNA fragments containing the sequence and the linearized plasmid were excised and purified by using a Qiaquick gel extraction kit (Qiagen, Calif.). The fragments of interest were ligated at a ratio of 3:1 (vector to insert). Ligation reactions using T4 DNA ligase (New England Biolabs, Mass.) were carried out at 16° C. for 16 hours. The ligated DNAs were transformed into competent cells of the E. coli strain DH5 alpha by using the heat shock method. The transformations were plated on LB plates containing 50 mg/l kanamycin (Sigma).

[0125] Individual colonies were grown overnight in five milliliters of LB broth containing 50 mg/l kanamycin at 37° C. Plasmid DNA was purified by using Qiaquick Mini Prep kits (Qiagen, Calif.).

EXAMPLE III TRANSFORMATION OF AGROBACTERIUM WITH THE EXPRESSION VECTOR

[0126] After the plasmid vector containing the gene was constructed, the vector was used to transform Agrobacterium tumefaciens cells expressing the gene products. The stock of Agrobacterium tumefaciens cells for transformation were made as described by Nagel et al. (1990) FEMS Microbiol Letts. 67: 325-328. Agrobacterium strain ABI was grown in 250 ml LB medium (Sigma) overnight at 28° C. with shaking until an absorbance (A₆₀₀) of 0.5-1.0 was reached. Cells were harvested by centrifugation at 4,000 × g for 15 min at 4° C. Cells were then resuspended in 250 μl chilled buffer (1 mM HEPES, pH adjusted to 7.0 with KOH). Cells were centrifuged again as described above and resuspended in 125 μl chilled buffer. Cells were then centrifuged and resuspended two more times in the same HEPES buffer as described above at a volume of 100 μl and 750 μl, respectively. Resuspended cells were then distributed into 40 μl aliquots, quickly frozen in liquid nitrogen, and stored at −80° C.

[0127]Agrobacterium cells were transformed with plasmids prepared as described above following the protocol described by Nagel et al. For each DNA construct to be transformed, 50-100 ng DNA (generally resuspended in 10 mM Tris-HCl, 1 mM EDTA, pH 8.0) was mixed with 40 μl of Agrobacterium cells. The DNA/cell mixture was then transferred to a chilled cuvette with a 2mm electrode gap and subject to a 2.5 kV charge dissipated at 25 μF and 200 μF using a Gene Pulser II apparatus (Bio-Rad). After electroporation, cells were immediately resuspended in 1.0 ml LB and allowed to recover without antibiotic selection for 2-4 hours at 28° C. in a shaking incubator. After recovery, cells were plated onto selective medium of LB broth containing 100 μg/ml spectinomycin (Sigma) and incubated for 24-48 hours at 28° C. Single colonies were then picked and inoculated in fresh medium. The presence of the plasmid construct was verified by PCR amplification and sequence analysis.

EXAMPLE IV TRANSFORMATION OF ARABIDOPSIS PLANTS WITH AGROBACTERIUM TUMEFACIENS WITH EXPRESSION VECTOR

[0128] After transformation of Agrobacterium tumefaciens with plasmid vectors containing the gene, single Agrobacterium colonies were identified, propagated, and used to transform Arabidopsis plants. Briefly, 500 ml cultures of LB medium containing 50 mg/l kanamycin were inoculated with the colonies and grown at 28° C. with shaking for 2 days until an absorbance (A₆₀₀) of >2.0 is reached. Cells were then harvested by centrifugation at 4,000 × g for 10 min, and resuspended in infiltration medium (½× Murashige and Skoog salts (Sigma), 1 × Gamborg's B-5 vitamins (Sigma), 5.0% (w/v) sucrose (Sigma), 0.044 μM benzylamino purine (Sigma), 200 μl/L Silwet L-77 (Lehle Seeds) until an absorbance (A600) of 0.8 was reached.

[0129] Prior to transformation, Arabidopsis thaliana seeds (ecotype Columbia) were sown at a density of −10 plants per 4″ pot onto Pro-Mix BX potting medium (Hummert International) covered with fiberglass mesh (18 mm×16 mm). Plants were grown under continuous illumination (50-75 μE/m²/sec) at 22-23° C. with 65-70% relative humidity. After about 4 weeks, primary inflorescence stems (bolts) are cut off to encourage growth of multiple secondary bolts. After flowering of the mature secondary bolts, plants were prepared for transformation by removal of all siliques and opened flowers.

[0130] The pots were then immersed upside down in the mixture of Agrobacterium infiltration medium as described above for 30 sec, and placed on their sides to allow draining into a 1′×2′ flat surface covered with plastic wrap. After 24 h, the plastic wrap was removed and pots are turned upright. The immersion procedure was repeated one week later, for a total of two immersions per pot. Seeds were then collected from each transformation pot and analyzed following the protocol described below.

EXAMPLE V IDENTIFICATION OF ARABIDOPSIS PRIMARY TRANSFORMANTS

[0131] Seeds collected from the transformation pots were sterilized essentially as follows. Seeds were dispersed into in a solution containing 0.1% (v/v) Triton X-100 (Sigma) and sterile H₂O and washed by shaking the suspension for 20 min. The wash solution was then drained and replaced with fresh wash solution to wash the seeds for 20 min with shaking. After removal of the second wash solution, a solution containing 0.1% (v/v) Triton X-100 and 70% ethanol (Equistar) was added to the seeds and the suspension was shaken for 5 min. After removal of the ethanol/detergent solution, a solution containing 0.1% (v/v) Triton X-100 and 30% (v/v) bleach (Clorox) was added to the seeds, and the suspension was shaken for 10 min. After removal of the bleach/detergent solution, seeds were then washed five times in sterile distilled H₂O. The seeds were stored in the last wash water at 4° C. for 2 days in the dark before being plated onto antibiotic selection medium (1× Murashige and Skoog salts (pH adjusted to 5.7 with 1M KOH), 1× Gamborg's B-5 vitamins, 0.9% phytagar (Life Technologies), and 50 mg/l kanamycin). Seeds were germinated under continuous illumination (50-75 μE/m²/sec) at 22-23° C. After 7-10 days of growth under these conditions, kanamycin resistant primary transformants (Ti generation) were visible and obtained. These seedlings were transferred first to fresh selection plates where the seedlings continued to grow for 3-5 more days, and then to soil (Pro-Mix BX potting medium).

[0132] Primary transformants were crossed and progeny seeds (T₂) collected; kanamycin resistant seedlings were selected and analyzed. The expression levels of the recombinant polynucleotides in the transformants varies from about a 5% expression level increase to a least a 100% expression level increase. Similar observations are made with respect to polypeptide level expression.

EXAMPLE VI IDENTIFICATION OF ARABIDOPSIS PLANTS WITH TRANSCRIPTION FACTOR GENE KNOCKOUTS

[0133] The screening of insertion mutagenized Arabidopsis collections for null mutants in a known target gene was essentially as described in Krysan et al (1999) Plant Cell 11:2283-2290. Briefly, gene-specific primers, nested by 5-250 base pairs to each other, were designed from the 5′ and 3′ regions of a known target gene. Similarly, nested sets of primers were also created specific to each of the T-DNA or transposon ends (the “right” and “left” borders). All possible combinations of gene specific and T-DNA/transposon primers were used to detect by PCR an insertion event within or close to the target gene. The amplified DNA fragments were then sequenced which allows the precise determination of the T-DNA/transposon insertion point relative to the target gene. Insertion events within the coding or intervening sequence of the genes were deconvoluted from a pool comprising a plurality of insertion events to a single unique mutant plant for functional characterization. The method is described in more detail in Yu and Adam, U.S. application Ser. No. 09/177,733 filed Oct. 23, 1998.

EXAMPLE VII IDENTIFICATION OF MODIFIED FLOWERING TIME OR FLOWERING PERIOD IN OVEREXPRESSOR OR GENE KNOCKOUT PLANTS

[0134] Experiments were performed to identify those transformants or knockouts that exhibited a modified flowering time or flowering period phenotype. For such studies, the transformants were observed for modified phenotypes over the period from seedling growth to sensecense. The plants were grown under continous light conditions at 20-25° C.

[0135] We observed that plants overexpressing G2010 (SEQ I) Nos. 7 and 8) constitutively (three independent T2 populations having 6 plants in one population and 16 plants in each of the other two) flowered approximately 1 week earlier than control plants transformed with an empty transformation vector under the control of the 35S promoter. The primary shoot of 35S::G2010 plants produced 5-6 rosette leaves before bolting, compared to 8-10 rosette leaves in controls. Flower buds were first visible 12-14 days after sowing in 35S::G2010 plants compared with approximately 20 days for wild type. At 20 days the 35S::G2010 plants have open flowers at this time whereas the wild type has yet to generate an inflorescence.

[0136] We identified an additional gene that is related based on sequence identity and therefore may also be suitable for creating an early flowering phenotype. The gene is G2347 (SEQ ID Nos: 19 and 20). G2347 shares about 52% sequence identity over the whole sequence length and 95% sequence identity over the conserved domain.

[0137] We also observed that a population of homozygous plants which carried a T-DNA insertion in the coding region of G1037 (SEQ ID Nos: 9 and 10) had a modified flowering phenotype. Knockout G1037 plants (12 individuals in total), grown under continuous light conditions at 20-25° C., produced 4-7 primary rosette leaves before bolting compared to 8-9 rosette leaves in controls harbouring an empty transformation vector. Flower buds were first visible in knockout G1037 plants approximately 1 week earlier than in controls. Early flowering was also noted in knockout G1037 plants grown for 1 week in continous light followed by subsequent growth under 12 hours light. At 28 days the flower buds are visible in the knockout G1037 but not the controls.

[0138] We also identified additional genes that are related based on sequence identity and therefore may also be suitable for observing an early flowering phenotype. The gene is G722 (SEQ ID Nos: 21 and 22) and G1493 (SEQ ID Nos. 23 and 24). G722 shares about 66% sequence identity over the whole sequence length compared with G1037 and 78% sequence identity over the conserved domain compared with G1037. G1493 shares about 40% sequence identity over the whole sequence length and 78% sequence identity over the conserved domain.

[0139] Further, we identified additional overexpressor plants that also had a modified flowering phenotype. Table 3 shows the phenotypes observed for particular overexpressor or knockout plants and provides the SEQ ID No., the internal reference code (GID), whether a knockout or overexpressor plant was analyzed and the observed phenotype. TABLE 3 Knockout (KO) or SEQ ID No. GID overexpressor (OE) Phenotype 3 G1760 OE Early flowering time 1 G590 OE Early flowering time 5 G1820 OE Early flowering time

[0140] G152 (SEQ ID Nos. 13 and 14), G153 (SEQ ID Nos. 15 and 16), and G860 (SEQ ID Nos. 17 and 18) were all found to be related to G1760(SEQ ID Nos. 3 and 4). G152 shares about 75% sequence identity over the whole sequence length and 93% sequence identity over the conserved domain. G153 shares about 60% sequence identity over the whole sequence length and 85% sequence identity over the conserved domain. G860 shares about 61% sequence identity over the whole sequence length and 85% sequence identity over the conserved domain.

[0141] Another knockout G1947 (SEQ ID Nos: 11 and 12) showed an extended flowering period or extrended reproductive phase. A control plant population produced flowers for approximately 15 days whereas the overexpressor plant population flowered for approximately 30 days due to a longer retention period of the flowers or a delay in senescense..

[0142] By altering the expression levels of the genes of the present invention a variety of plant traits can be altered. For example, plants with accelerated, delayed, or inducible flowering times may be generated. Alternatively the vernalization period or flower retention period or an increase in the total number of flowers may be achieved.

[0143] (1) Accelerated flowering

[0144] A number of Arabidopsis genes have already been shown to accelerate flowering when constitutively expressed. These include LEAFY, APETALA1 and CONSTANS. In these cases, however, the early flowering plants showed undesirable side effects such as extreme dwarfing, infertility, or premature termination of shoot meristem growth (Mandel, M. et al., 1995, Nature 377, 522-524; Weigel, D. and Nilsson, O., 1995, Nature 377, 495-500; Simon et al., 1996, Nature 384, 59-62, Onouchi et al., 2000, Plant Cell 12, 885-900). Most modern crop varieties are the result of extensive breeding programs. Many generations of backcrossing may be required to introduce desired traits. Systems that accelerate flowering could have valuable applications in such programs since they allow much faster generation times. Additionally, in some instances, a faster generation time might allow additional harvests of a crop to be made within a given growing season.

[0145] With the advent of transformation systems for tree species such as oil palm and Eucalyptus, forest biotechnology is a growing area of interest. Acceleration of flowering, again, might reduce generation times and make breeding programs feasible which would otherwise be impossible. That this is a real possibility has already been demonstrated in aspen, a tree species that usually takes 8-20 years to flower. Transgenic aspen that overexpress the Arabidopsis LFY gene flower after only 5 months. The flowers produced by these young aspen plants, however, were sterile; the challenge of producing fertile early flowering trees therefore still remains (Weigel, D. and Nilsson, O., 1995, Nature 377, 495-500).

[0146] (2) Delayed Flowering

[0147] In species such as sugarbeet where the vegetative parts of the plants constitute the crop and the reproductive tissues are discarded, it would be advantageous to delay or prevent flowering. Extending vegetative development could bring about large increases in yields. Additionally, a major concern is the escape of transgenic pollen from GMOs to wild species or so-called organic crops. Systems that prevent vegetative transgenic crops from flowering would eliminate this worry.

[0148] (3) Inducible Flowering

[0149] By regulating the expression of genes of the invention in transgenic plants using inducible promoters, flowering could be triggered by application of an inducer chemical. This would allow flowering to be synchronized across a crop and facilitate more efficient harvesting. Such inducible systems could be used to tune the flowering of crop varieties to different latitudes. At present, species such as soybean and cotton are available as a series of maturity groups that are suitable for different latitudes on the basis of their flowering time (which is governed by day-length). A system in which flowering could be chemically controlled would allow a single high-yielding Northern maturity group to be grown at any latitude. In Southern regions such plants could be grown for longer, thereby increasing yields, before flowering was induced. In more Northern areas, the induction would be used to ensure that the crop flowers prior to the first winter frosts.

[0150] Currently, the existence of a series of maturity groups for different latitudes represents a major barrier to the introduction of new valuable traits. Any trait (e.g. disease resistance) has to be bred into each of the different maturity groups separately; a laborious and costly exercise. The availability of single strain, which could be grown at any latitude, would therefore greatly increase the potential for introducing new traits to crop species such as soybean and cotton. An application might also exist in fruit trees such as apple, in which flowering shoots lie dormant for long periods, before flowers develop. Genes which accelerate flowering might be applied to synchronized flower development and break this dormancy.

[0151] (4) Vernalization

[0152] Specific applications for some of these genes relate to their potential roles in the vernalization response. For many crop species, high yielding winter-varieties can only be grown in temperate regions where the winter season is prolonged and cold enough to elicit a vernalization response. Constitutive expression may compensate for a vernalization treatment in late-flowering ecotypes. Winter varieties of wheat, for instance, which over-express a gene (or the wheat ortholog) might then be grown in areas like Southern California which would otherwise be too warm to allow effective vernalization. A second application for this system is in cherry (Prunus). Locally grown cherries are unavailable in the early Californian spring since the winters are too warm for vernalization to occur.

[0153] All references, publications, patents and other documents herein are incorporated by reference in their entirety for all purposes. Although the invention has been described with reference to the embodiments and examples above, it should be understood that various modifications can be made without departing from the spirit of the invention.

1 24 1 1292 DNA Arabidopsis thaliana CDS (102)..(1223) G590 1 tcgacagaca ctctccctct ctccatgccc ataaaatctc aaagactgtt taaaaaaaaa 60 aatgttttag ctttaactgc tttttttttg ttgttggtgt a atg ata tca cag aga 116 Met Ile Ser Gln Arg 1 5 gaa gaa aga gaa gag aag aag cag aga gtg atg gga gat aag aaa ttg 164 Glu Glu Arg Glu Glu Lys Lys Gln Arg Val Met Gly Asp Lys Lys Leu 10 15 20 att tca tct tct tct tct tcc tcg gtt tac gat act cgt atc aat cat 212 Ile Ser Ser Ser Ser Ser Ser Ser Val Tyr Asp Thr Arg Ile Asn His 25 30 35 cat ctt cat cat cct ccg tct tct tcc gac gaa atc tct cag ttt ctc 260 His Leu His His Pro Pro Ser Ser Ser Asp Glu Ile Ser Gln Phe Leu 40 45 50 cgg cat att ttc gac cgt tct tct cct tta cct tct tac tac tcc ccg 308 Arg His Ile Phe Asp Arg Ser Ser Pro Leu Pro Ser Tyr Tyr Ser Pro 55 60 65 gcg acg act aca acg acg gcg tct ttg att ggt gtg cac ggg agc ggt 356 Ala Thr Thr Thr Thr Thr Ala Ser Leu Ile Gly Val His Gly Ser Gly 70 75 80 85 gac cca cat gca gat aac tcg aga agt ctc gtt tct cat cat cca ccg 404 Asp Pro His Ala Asp Asn Ser Arg Ser Leu Val Ser His His Pro Pro 90 95 100 tca gat tct gtg ctt atg tcg aaa cgt gtc gga gat ttc tct gag gtt 452 Ser Asp Ser Val Leu Met Ser Lys Arg Val Gly Asp Phe Ser Glu Val 105 110 115 tta atc ggc gga gga tca ggc tca gcc gcc gcg tgt ttt ggt ttc tcc 500 Leu Ile Gly Gly Gly Ser Gly Ser Ala Ala Ala Cys Phe Gly Phe Ser 120 125 130 ggt ggt ggt aat aat aac aac gtt caa gga aat agc tct ggg act cga 548 Gly Gly Gly Asn Asn Asn Asn Val Gln Gly Asn Ser Ser Gly Thr Arg 135 140 145 gta tcg tct tct tcc gtt gga gct agt ggc aac gag aca gat gag tat 596 Val Ser Ser Ser Ser Val Gly Ala Ser Gly Asn Glu Thr Asp Glu Tyr 150 155 160 165 gac tgt gaa agc gag gaa gga gga gaa gct gta gtt gat gaa gct ccc 644 Asp Cys Glu Ser Glu Glu Gly Gly Glu Ala Val Val Asp Glu Ala Pro 170 175 180 tct tcc aag tca ggt cct tct tct cgt agt tca tct aaa aga tgc aga 692 Ser Ser Lys Ser Gly Pro Ser Ser Arg Ser Ser Ser Lys Arg Cys Arg 185 190 195 gct gct gaa gtt cat aat ctc tct gag aag agg agg aga agt aga att 740 Ala Ala Glu Val His Asn Leu Ser Glu Lys Arg Arg Arg Ser Arg Ile 200 205 210 aat gaa aaa atg aaa gct tta caa agt ctc atc cct aat tca aat aag 788 Asn Glu Lys Met Lys Ala Leu Gln Ser Leu Ile Pro Asn Ser Asn Lys 215 220 225 acg gat aag gct tca atg ctt gat gaa gcc att gag tat ctg aaa cag 836 Thr Asp Lys Ala Ser Met Leu Asp Glu Ala Ile Glu Tyr Leu Lys Gln 230 235 240 245 ctt cag ctc caa gtt cag atg ttg act atg aga aat gga ata aac ttg 884 Leu Gln Leu Gln Val Gln Met Leu Thr Met Arg Asn Gly Ile Asn Leu 250 255 260 cat cct ttg tgt tta cct gga act aca tta cac cca ttg caa ctc tct 932 His Pro Leu Cys Leu Pro Gly Thr Thr Leu His Pro Leu Gln Leu Ser 265 270 275 cag att cga ccc cct gaa gca acc aat gat cct ctg ctt aat cat acc 980 Gln Ile Arg Pro Pro Glu Ala Thr Asn Asp Pro Leu Leu Asn His Thr 280 285 290 aat cag ttt gct tcg act tct aat gca ccg gaa atg atc aat act gtg 1028 Asn Gln Phe Ala Ser Thr Ser Asn Ala Pro Glu Met Ile Asn Thr Val 295 300 305 gct tct tca tac gct ttg gaa cct tct att cgc agt cac ttt gga cct 1076 Ala Ser Ser Tyr Ala Leu Glu Pro Ser Ile Arg Ser His Phe Gly Pro 310 315 320 325 ttc cct ctc ctt act tca ccc gtg gag atg agt cgg gaa ggt ggg tta 1124 Phe Pro Leu Leu Thr Ser Pro Val Glu Met Ser Arg Glu Gly Gly Leu 330 335 340 act cat cca agg ttg aac att ggt cat tcc aac gca aac ata acc ggg 1172 Thr His Pro Arg Leu Asn Ile Gly His Ser Asn Ala Asn Ile Thr Gly 345 350 355 gaa caa gct ctg ttt gat gga caa cct gac cta aaa gat cga att act 1220 Glu Gln Ala Leu Phe Asp Gly Gln Pro Asp Leu Lys Asp Arg Ile Thr 360 365 370 tga acagtgtccc aacttcggga tctctatgtg ttcttgtttc ttagaacgca 1273 agccataaag ctgtctgac 1292 2 373 PRT Arabidopsis thaliana 2 Met Ile Ser Gln Arg Glu Glu Arg Glu Glu Lys Lys Gln Arg Val Met 1 5 10 15 Gly Asp Lys Lys Leu Ile Ser Ser Ser Ser Ser Ser Ser Val Tyr Asp 20 25 30 Thr Arg Ile Asn His His Leu His His Pro Pro Ser Ser Ser Asp Glu 35 40 45 Ile Ser Gln Phe Leu Arg His Ile Phe Asp Arg Ser Ser Pro Leu Pro 50 55 60 Ser Tyr Tyr Ser Pro Ala Thr Thr Thr Thr Thr Ala Ser Leu Ile Gly 65 70 75 80 Val His Gly Ser Gly Asp Pro His Ala Asp Asn Ser Arg Ser Leu Val 85 90 95 Ser His His Pro Pro Ser Asp Ser Val Leu Met Ser Lys Arg Val Gly 100 105 110 Asp Phe Ser Glu Val Leu Ile Gly Gly Gly Ser Gly Ser Ala Ala Ala 115 120 125 Cys Phe Gly Phe Ser Gly Gly Gly Asn Asn Asn Asn Val Gln Gly Asn 130 135 140 Ser Ser Gly Thr Arg Val Ser Ser Ser Ser Val Gly Ala Ser Gly Asn 145 150 155 160 Glu Thr Asp Glu Tyr Asp Cys Glu Ser Glu Glu Gly Gly Glu Ala Val 165 170 175 Val Asp Glu Ala Pro Ser Ser Lys Ser Gly Pro Ser Ser Arg Ser Ser 180 185 190 Ser Lys Arg Cys Arg Ala Ala Glu Val His Asn Leu Ser Glu Lys Arg 195 200 205 Arg Arg Ser Arg Ile Asn Glu Lys Met Lys Ala Leu Gln Ser Leu Ile 210 215 220 Pro Asn Ser Asn Lys Thr Asp Lys Ala Ser Met Leu Asp Glu Ala Ile 225 230 235 240 Glu Tyr Leu Lys Gln Leu Gln Leu Gln Val Gln Met Leu Thr Met Arg 245 250 255 Asn Gly Ile Asn Leu His Pro Leu Cys Leu Pro Gly Thr Thr Leu His 260 265 270 Pro Leu Gln Leu Ser Gln Ile Arg Pro Pro Glu Ala Thr Asn Asp Pro 275 280 285 Leu Leu Asn His Thr Asn Gln Phe Ala Ser Thr Ser Asn Ala Pro Glu 290 295 300 Met Ile Asn Thr Val Ala Ser Ser Tyr Ala Leu Glu Pro Ser Ile Arg 305 310 315 320 Ser His Phe Gly Pro Phe Pro Leu Leu Thr Ser Pro Val Glu Met Ser 325 330 335 Arg Glu Gly Gly Leu Thr His Pro Arg Leu Asn Ile Gly His Ser Asn 340 345 350 Ala Asn Ile Thr Gly Glu Gln Ala Leu Phe Asp Gly Gln Pro Asp Leu 355 360 365 Lys Asp Arg Ile Thr 370 3 1038 DNA Arabidopsis thaliana CDS (50)..(736) G1760 3 ccctaaaaaa gagaagaacc agaggagatt caattagagg ataaaattg atg gga aga 58 Met Gly Arg 1 ggg aag att gtg atc caa agg atc gat gat tca acg agt aga caa gtc 106 Gly Lys Ile Val Ile Gln Arg Ile Asp Asp Ser Thr Ser Arg Gln Val 5 10 15 act ttc tcc aaa cga aga aag ggc ctt atc aag aaa gcc aaa gag cta 154 Thr Phe Ser Lys Arg Arg Lys Gly Leu Ile Lys Lys Ala Lys Glu Leu 20 25 30 35 gct att ctc tgt gat gcc gag gtc ggt ctc atc atc ttc tct agc acc 202 Ala Ile Leu Cys Asp Ala Glu Val Gly Leu Ile Ile Phe Ser Ser Thr 40 45 50 gga aag ctc tat gac ttt gca agc tcc agc atg aag tcg gtt att gat 250 Gly Lys Leu Tyr Asp Phe Ala Ser Ser Ser Met Lys Ser Val Ile Asp 55 60 65 aga tac aac aag agc aag atc gag caa caa caa cta ttg aac ccc gca 298 Arg Tyr Asn Lys Ser Lys Ile Glu Gln Gln Gln Leu Leu Asn Pro Ala 70 75 80 tca gaa gtc aag ttt tgg cag aga gaa gct gct gtt cta aga caa gaa 346 Ser Glu Val Lys Phe Trp Gln Arg Glu Ala Ala Val Leu Arg Gln Glu 85 90 95 ctg cat gct ttg caa gaa aat cat cgg caa atg atg gga gaa cag cta 394 Leu His Ala Leu Gln Glu Asn His Arg Gln Met Met Gly Glu Gln Leu 100 105 110 115 aat ggt tta agt gtt aac gag cta aac agt ctt gag aat caa att gag 442 Asn Gly Leu Ser Val Asn Glu Leu Asn Ser Leu Glu Asn Gln Ile Glu 120 125 130 ata agt ttg cgt gga att cgt atg aga aag gaa caa ctg ttg act caa 490 Ile Ser Leu Arg Gly Ile Arg Met Arg Lys Glu Gln Leu Leu Thr Gln 135 140 145 gaa atc caa gaa cta agc caa aag agg aat ctt att cat cag gaa aac 538 Glu Ile Gln Glu Leu Ser Gln Lys Arg Asn Leu Ile His Gln Glu Asn 150 155 160 ctc gat tta tct agg aaa gta caa cgg att cat caa gaa aat gtg gag 586 Leu Asp Leu Ser Arg Lys Val Gln Arg Ile His Gln Glu Asn Val Glu 165 170 175 ctc tac aag aag gct tat atg gca aac aca aac ggg ttt aca cac cgt 634 Leu Tyr Lys Lys Ala Tyr Met Ala Asn Thr Asn Gly Phe Thr His Arg 180 185 190 195 gaa gta gct gtt gcg gat gat gaa tca cac act cag att cgg ctg caa 682 Glu Val Ala Val Ala Asp Asp Glu Ser His Thr Gln Ile Arg Leu Gln 200 205 210 cta agc cag cct gaa cat tcc gat tat gac act cca cca aga gca aac 730 Leu Ser Gln Pro Glu His Ser Asp Tyr Asp Thr Pro Pro Arg Ala Asn 215 220 225 gaa taa cagagagatt gaagttggaa gataccatga tgttgaagaa cactccaaag 786 Glu gccttggttt gaataaggtt cttgaactgg aaacctctat acaccaagcc acgtacgata 846 agcagcatgg ttcttctaac atagtcatat tttcaatcct aaatataatt aaagcatata 906 taattaaaat ccggtgttgt tatactcatc ttgagtatta atattgtact tgtttataac 966 catagattcg tcaattaata gagaaaaatc atatgaatta ttatccaaaa aaaaaaaaaa 1026 aaaaaaaaaa aa 1038 4 228 PRT Arabidopsis thaliana 4 Met Gly Arg Gly Lys Ile Val Ile Gln Arg Ile Asp Asp Ser Thr Ser 1 5 10 15 Arg Gln Val Thr Phe Ser Lys Arg Arg Lys Gly Leu Ile Lys Lys Ala 20 25 30 Lys Glu Leu Ala Ile Leu Cys Asp Ala Glu Val Gly Leu Ile Ile Phe 35 40 45 Ser Ser Thr Gly Lys Leu Tyr Asp Phe Ala Ser Ser Ser Met Lys Ser 50 55 60 Val Ile Asp Arg Tyr Asn Lys Ser Lys Ile Glu Gln Gln Gln Leu Leu 65 70 75 80 Asn Pro Ala Ser Glu Val Lys Phe Trp Gln Arg Glu Ala Ala Val Leu 85 90 95 Arg Gln Glu Leu His Ala Leu Gln Glu Asn His Arg Gln Met Met Gly 100 105 110 Glu Gln Leu Asn Gly Leu Ser Val Asn Glu Leu Asn Ser Leu Glu Asn 115 120 125 Gln Ile Glu Ile Ser Leu Arg Gly Ile Arg Met Arg Lys Glu Gln Leu 130 135 140 Leu Thr Gln Glu Ile Gln Glu Leu Ser Gln Lys Arg Asn Leu Ile His 145 150 155 160 Gln Glu Asn Leu Asp Leu Ser Arg Lys Val Gln Arg Ile His Gln Glu 165 170 175 Asn Val Glu Leu Tyr Lys Lys Ala Tyr Met Ala Asn Thr Asn Gly Phe 180 185 190 Thr His Arg Glu Val Ala Val Ala Asp Asp Glu Ser His Thr Gln Ile 195 200 205 Arg Leu Gln Leu Ser Gln Pro Glu His Ser Asp Tyr Asp Thr Pro Pro 210 215 220 Arg Ala Asn Glu 225 5 609 DNA Arabidopsis thaliana CDS (1)..(609) G1820 5 atg gct gag aac aac aac aac aac ggc gac aac atg aac aac gac aac 48 Met Ala Glu Asn Asn Asn Asn Asn Gly Asp Asn Met Asn Asn Asp Asn 1 5 10 15 cac cag caa cca ccg tcg tac tcg cag ctg ccg ccg atg gca tca tcc 96 His Gln Gln Pro Pro Ser Tyr Ser Gln Leu Pro Pro Met Ala Ser Ser 20 25 30 aac cct cag tta cgt aat tac tgg att gag cag atg gaa acc gtc tcg 144 Asn Pro Gln Leu Arg Asn Tyr Trp Ile Glu Gln Met Glu Thr Val Ser 35 40 45 gat ttc aaa aac cgt cag ctt cca ttg gct cga att aag aag atc atg 192 Asp Phe Lys Asn Arg Gln Leu Pro Leu Ala Arg Ile Lys Lys Ile Met 50 55 60 aag gct gat cca gat gtg cac atg gtc tcc gca gag gct ccg atc atc 240 Lys Ala Asp Pro Asp Val His Met Val Ser Ala Glu Ala Pro Ile Ile 65 70 75 80 ttc gca aag gct tgc gaa atg ttc atc gtt gat ctc acg atg cgg tcg 288 Phe Ala Lys Ala Cys Glu Met Phe Ile Val Asp Leu Thr Met Arg Ser 85 90 95 tgg ctc aaa gcc gag gag aac aaa cgc cac acg ctt cag aaa tcg gat 336 Trp Leu Lys Ala Glu Glu Asn Lys Arg His Thr Leu Gln Lys Ser Asp 100 105 110 atc tcc aac gca gtg gct agc tct ttc acc tac gat ttc ctt ctt gat 384 Ile Ser Asn Ala Val Ala Ser Ser Phe Thr Tyr Asp Phe Leu Leu Asp 115 120 125 gtt gtc cct aag gac gag tct atc gcc acc gct gat cct ggc ttt gtg 432 Val Val Pro Lys Asp Glu Ser Ile Ala Thr Ala Asp Pro Gly Phe Val 130 135 140 gct atg cca cat cct gac ggt gga gga gta ccg caa tat tat tat cca 480 Ala Met Pro His Pro Asp Gly Gly Gly Val Pro Gln Tyr Tyr Tyr Pro 145 150 155 160 ccg gga gtg gtg atg gga act cct atg gtt ggt agt gga atg tac gcg 528 Pro Gly Val Val Met Gly Thr Pro Met Val Gly Ser Gly Met Tyr Ala 165 170 175 cca tcg cag gcg tgg cca gca gcg gct ggt gac ggg gag gat gat gct 576 Pro Ser Gln Ala Trp Pro Ala Ala Ala Gly Asp Gly Glu Asp Asp Ala 180 185 190 gag gat aat gga gga aac ggc ggc gga aat tga 609 Glu Asp Asn Gly Gly Asn Gly Gly Gly Asn 195 200 6 202 PRT Arabidopsis thaliana 6 Met Ala Glu Asn Asn Asn Asn Asn Gly Asp Asn Met Asn Asn Asp Asn 1 5 10 15 His Gln Gln Pro Pro Ser Tyr Ser Gln Leu Pro Pro Met Ala Ser Ser 20 25 30 Asn Pro Gln Leu Arg Asn Tyr Trp Ile Glu Gln Met Glu Thr Val Ser 35 40 45 Asp Phe Lys Asn Arg Gln Leu Pro Leu Ala Arg Ile Lys Lys Ile Met 50 55 60 Lys Ala Asp Pro Asp Val His Met Val Ser Ala Glu Ala Pro Ile Ile 65 70 75 80 Phe Ala Lys Ala Cys Glu Met Phe Ile Val Asp Leu Thr Met Arg Ser 85 90 95 Trp Leu Lys Ala Glu Glu Asn Lys Arg His Thr Leu Gln Lys Ser Asp 100 105 110 Ile Ser Asn Ala Val Ala Ser Ser Phe Thr Tyr Asp Phe Leu Leu Asp 115 120 125 Val Val Pro Lys Asp Glu Ser Ile Ala Thr Ala Asp Pro Gly Phe Val 130 135 140 Ala Met Pro His Pro Asp Gly Gly Gly Val Pro Gln Tyr Tyr Tyr Pro 145 150 155 160 Pro Gly Val Val Met Gly Thr Pro Met Val Gly Ser Gly Met Tyr Ala 165 170 175 Pro Ser Gln Ala Trp Pro Ala Ala Ala Gly Asp Gly Glu Asp Asp Ala 180 185 190 Glu Asp Asn Gly Gly Asn Gly Gly Gly Asn 195 200 7 525 DNA Arabidopsis thaliana CDS (1)..(525) G2010 7 atg gag ggt aag aga tca caa gga caa ggt tac atg aaa aag aag tct 48 Met Glu Gly Lys Arg Ser Gln Gly Gln Gly Tyr Met Lys Lys Lys Ser 1 5 10 15 tac ctt gtg gaa gaa gat atg gag act gat acg gat gaa gaa gag gaa 96 Tyr Leu Val Glu Glu Asp Met Glu Thr Asp Thr Asp Glu Glu Glu Glu 20 25 30 gta ggt agg gat aga gtt aga ggg tct aga ggt agc atc aat cgt ggt 144 Val Gly Arg Asp Arg Val Arg Gly Ser Arg Gly Ser Ile Asn Arg Gly 35 40 45 ggc tcg ttg cgg ctt tgc caa gta gat aga tgc aca gct gat atg aaa 192 Gly Ser Leu Arg Leu Cys Gln Val Asp Arg Cys Thr Ala Asp Met Lys 50 55 60 gag gca aaa ctg tat cac cgg aga cac aaa gtg tgt gaa gtt cat gca 240 Glu Ala Lys Leu Tyr His Arg Arg His Lys Val Cys Glu Val His Ala 65 70 75 80 aag gca tct tct gtc ttt ctc tca gga ctt aac caa cgc ttt tgt caa 288 Lys Ala Ser Ser Val Phe Leu Ser Gly Leu Asn Gln Arg Phe Cys Gln 85 90 95 caa tgc agt agg ttt cat gac ctc caa gag ttt gat gaa gct aag aga 336 Gln Cys Ser Arg Phe His Asp Leu Gln Glu Phe Asp Glu Ala Lys Arg 100 105 110 agt tgc agg agg cgc tta gct gga cac aat gag cga aga agg aag agc 384 Ser Cys Arg Arg Arg Leu Ala Gly His Asn Glu Arg Arg Arg Lys Ser 115 120 125 tct ggt gag agt act tat gga gaa gga tca ggt cgg aga gga atc aat 432 Ser Gly Glu Ser Thr Tyr Gly Glu Gly Ser Gly Arg Arg Gly Ile Asn 130 135 140 ggt cag gtg gtg atg cag aat caa gaa aga tca agg gta gag atg aca 480 Gly Gln Val Val Met Gln Asn Gln Glu Arg Ser Arg Val Glu Met Thr 145 150 155 160 ctt cct atg cca aac tca tca ttc aag cga cca cag att aga tag 525 Leu Pro Met Pro Asn Ser Ser Phe Lys Arg Pro Gln Ile Arg 165 170 8 174 PRT Arabidopsis thaliana 8 Met Glu Gly Lys Arg Ser Gln Gly Gln Gly Tyr Met Lys Lys Lys Ser 1 5 10 15 Tyr Leu Val Glu Glu Asp Met Glu Thr Asp Thr Asp Glu Glu Glu Glu 20 25 30 Val Gly Arg Asp Arg Val Arg Gly Ser Arg Gly Ser Ile Asn Arg Gly 35 40 45 Gly Ser Leu Arg Leu Cys Gln Val Asp Arg Cys Thr Ala Asp Met Lys 50 55 60 Glu Ala Lys Leu Tyr His Arg Arg His Lys Val Cys Glu Val His Ala 65 70 75 80 Lys Ala Ser Ser Val Phe Leu Ser Gly Leu Asn Gln Arg Phe Cys Gln 85 90 95 Gln Cys Ser Arg Phe His Asp Leu Gln Glu Phe Asp Glu Ala Lys Arg 100 105 110 Ser Cys Arg Arg Arg Leu Ala Gly His Asn Glu Arg Arg Arg Lys Ser 115 120 125 Ser Gly Glu Ser Thr Tyr Gly Glu Gly Ser Gly Arg Arg Gly Ile Asn 130 135 140 Gly Gln Val Val Met Gln Asn Gln Glu Arg Ser Arg Val Glu Met Thr 145 150 155 160 Leu Pro Met Pro Asn Ser Ser Phe Lys Arg Pro Gln Ile Arg 165 170 9 1722 DNA Arabidopsis thaliana CDS (1)..(1722) G1037 9 atg act gtt gaa caa aat tta gaa gct ttg gat cag ttt cct gta gga 48 Met Thr Val Glu Gln Asn Leu Glu Ala Leu Asp Gln Phe Pro Val Gly 1 5 10 15 atg aga gtt ctt gct gtt gat gat gac caa act tgt ctc aaa atc ctt 96 Met Arg Val Leu Ala Val Asp Asp Asp Gln Thr Cys Leu Lys Ile Leu 20 25 30 gaa tct ctc ctt cgt cac tgc caa tac cat gta aca acg acg aac caa 144 Glu Ser Leu Leu Arg His Cys Gln Tyr His Val Thr Thr Thr Asn Gln 35 40 45 gca caa aag gct tta gag tta ttg aga gag aac aag aac aag ttt gat 192 Ala Gln Lys Ala Leu Glu Leu Leu Arg Glu Asn Lys Asn Lys Phe Asp 50 55 60 ctg gtt att agt gat gtt gac atg cct gac atg gat ggt ttc aaa ctc 240 Leu Val Ile Ser Asp Val Asp Met Pro Asp Met Asp Gly Phe Lys Leu 65 70 75 80 ctt gag ctt gtt ggt ctt gaa atg gac cta cct gtc ata atg ttg tct 288 Leu Glu Leu Val Gly Leu Glu Met Asp Leu Pro Val Ile Met Leu Ser 85 90 95 gcg cat agt gat cca aag tat gtg atg aag gga gtt act cat ggt gct 336 Ala His Ser Asp Pro Lys Tyr Val Met Lys Gly Val Thr His Gly Ala 100 105 110 tgt gat tat cta ctg aag ccg gtt cgt att gag gag ttg aag aac ata 384 Cys Asp Tyr Leu Leu Lys Pro Val Arg Ile Glu Glu Leu Lys Asn Ile 115 120 125 tgg caa cat gtc gtg aga agt aga ttt gat aag aac cgt ggg agt aat 432 Trp Gln His Val Val Arg Ser Arg Phe Asp Lys Asn Arg Gly Ser Asn 130 135 140 aat aat ggt gat aag aga gat gga tca ggt aat gaa ggt gtt ggg aat 480 Asn Asn Gly Asp Lys Arg Asp Gly Ser Gly Asn Glu Gly Val Gly Asn 145 150 155 160 tct gat ccg aac aat ggg aaa ggt aat aga aaa cgt aaa gat cag tat 528 Ser Asp Pro Asn Asn Gly Lys Gly Asn Arg Lys Arg Lys Asp Gln Tyr 165 170 175 aat gaa gat gag gat gag gat aga gat gat aat gat gat tcg tgt gct 576 Asn Glu Asp Glu Asp Glu Asp Arg Asp Asp Asn Asp Asp Ser Cys Ala 180 185 190 caa aag aag caa cgt gtt gtt tgg act gtt gag ctg cat aag aaa ttt 624 Gln Lys Lys Gln Arg Val Val Trp Thr Val Glu Leu His Lys Lys Phe 195 200 205 gtt gca gct gtt aac caa ttg gga tat gag aag gct atg cct aaa aag 672 Val Ala Ala Val Asn Gln Leu Gly Tyr Glu Lys Ala Met Pro Lys Lys 210 215 220 att ttg gat ctg atg aat gtt gag aag ctc act aga gaa aat gtg gcc 720 Ile Leu Asp Leu Met Asn Val Glu Lys Leu Thr Arg Glu Asn Val Ala 225 230 235 240 agt cat ctt cag aaa ttc cgc ctt tac ttg aag agg atc agt ggt gtg 768 Ser His Leu Gln Lys Phe Arg Leu Tyr Leu Lys Arg Ile Ser Gly Val 245 250 255 gct aat cag caa gct att atg gca aac tct gag tta cat ttt atg caa 816 Ala Asn Gln Gln Ala Ile Met Ala Asn Ser Glu Leu His Phe Met Gln 260 265 270 atg aat gga ctt gat ggt ttc cat cac cgc cca atc cct gtt gga tct 864 Met Asn Gly Leu Asp Gly Phe His His Arg Pro Ile Pro Val Gly Ser 275 280 285 ggt cag tac cat ggt ggg gct cct gca atg aga tct ttc cct cca aac 912 Gly Gln Tyr His Gly Gly Ala Pro Ala Met Arg Ser Phe Pro Pro Asn 290 295 300 ggg att ctt ggc aga ctc aat agc tct tcg ggg atc ggt gtc cgc agc 960 Gly Ile Leu Gly Arg Leu Asn Ser Ser Ser Gly Ile Gly Val Arg Ser 305 310 315 320 ctt tct tct cct cct gca gga atg ttc ttg caa aac cag acc gat atc 1008 Leu Ser Ser Pro Pro Ala Gly Met Phe Leu Gln Asn Gln Thr Asp Ile 325 330 335 gga aag ttt cac cat gtc tca tca ctt cct ctt aac cac agt gat gga 1056 Gly Lys Phe His His Val Ser Ser Leu Pro Leu Asn His Ser Asp Gly 340 345 350 gga aac ata ctt caa ggg ttg cca atg cct tta gag ttc gac cag ctt 1104 Gly Asn Ile Leu Gln Gly Leu Pro Met Pro Leu Glu Phe Asp Gln Leu 355 360 365 cag aca aac aac aac aaa agt aga aac atg aac agt aac aag agc att 1152 Gln Thr Asn Asn Asn Lys Ser Arg Asn Met Asn Ser Asn Lys Ser Ile 370 375 380 gct ggg acc tcc atg gct ttt cct agc ttc tct acg caa caa aac tcg 1200 Ala Gly Thr Ser Met Ala Phe Pro Ser Phe Ser Thr Gln Gln Asn Ser 385 390 395 400 ctc atc agt gct cct aat aac aat gtc gtg gtt cta gaa ggt cac cca 1248 Leu Ile Ser Ala Pro Asn Asn Asn Val Val Val Leu Glu Gly His Pro 405 410 415 caa gca act cct cca ggc ttc cca gga cac cag atc aat aaa cgt ttg 1296 Gln Ala Thr Pro Pro Gly Phe Pro Gly His Gln Ile Asn Lys Arg Leu 420 425 430 gag cat tgg tca aat gct gta tcc tct tcg act cac cct cct ccc ccg 1344 Glu His Trp Ser Asn Ala Val Ser Ser Ser Thr His Pro Pro Pro Pro 435 440 445 gca cat aac agt aat agt atc aat cat cag ttc gat gtc tct cca tta 1392 Ala His Asn Ser Asn Ser Ile Asn His Gln Phe Asp Val Ser Pro Leu 450 455 460 ccg cat tct aga ccc gac ccc ttg gaa tgg aac aat gtg tca tca agc 1440 Pro His Ser Arg Pro Asp Pro Leu Glu Trp Asn Asn Val Ser Ser Ser 465 470 475 480 tac tct ata cca ttc tgt gac tct gcc aat aca ttg agt tct cca gcc 1488 Tyr Ser Ile Pro Phe Cys Asp Ser Ala Asn Thr Leu Ser Ser Pro Ala 485 490 495 ttg gat aca aca aat ccc cga gct ttc tgt aga aac acg gac ttc gat 1536 Leu Asp Thr Thr Asn Pro Arg Ala Phe Cys Arg Asn Thr Asp Phe Asp 500 505 510 tca aac aca aat gtg caa cct gga gtc ttt tat ggt cca tcc acg gat 1584 Ser Asn Thr Asn Val Gln Pro Gly Val Phe Tyr Gly Pro Ser Thr Asp 515 520 525 gct atg gct ctg ttg agt agt agt aac ccg aaa gaa ggg ttc gtc gta 1632 Ala Met Ala Leu Leu Ser Ser Ser Asn Pro Lys Glu Gly Phe Val Val 530 535 540 ggc caa cag aag tta cag agt ggt gga ttc atg gtt gca gat gct ggt 1680 Gly Gln Gln Lys Leu Gln Ser Gly Gly Phe Met Val Ala Asp Ala Gly 545 550 555 560 tcc tta gat gat ata gtc aac tcc acg atg aag cag gtg tga 1722 Ser Leu Asp Asp Ile Val Asn Ser Thr Met Lys Gln Val 565 570 10 573 PRT Arabidopsis thaliana 10 Met Thr Val Glu Gln Asn Leu Glu Ala Leu Asp Gln Phe Pro Val Gly 1 5 10 15 Met Arg Val Leu Ala Val Asp Asp Asp Gln Thr Cys Leu Lys Ile Leu 20 25 30 Glu Ser Leu Leu Arg His Cys Gln Tyr His Val Thr Thr Thr Asn Gln 35 40 45 Ala Gln Lys Ala Leu Glu Leu Leu Arg Glu Asn Lys Asn Lys Phe Asp 50 55 60 Leu Val Ile Ser Asp Val Asp Met Pro Asp Met Asp Gly Phe Lys Leu 65 70 75 80 Leu Glu Leu Val Gly Leu Glu Met Asp Leu Pro Val Ile Met Leu Ser 85 90 95 Ala His Ser Asp Pro Lys Tyr Val Met Lys Gly Val Thr His Gly Ala 100 105 110 Cys Asp Tyr Leu Leu Lys Pro Val Arg Ile Glu Glu Leu Lys Asn Ile 115 120 125 Trp Gln His Val Val Arg Ser Arg Phe Asp Lys Asn Arg Gly Ser Asn 130 135 140 Asn Asn Gly Asp Lys Arg Asp Gly Ser Gly Asn Glu Gly Val Gly Asn 145 150 155 160 Ser Asp Pro Asn Asn Gly Lys Gly Asn Arg Lys Arg Lys Asp Gln Tyr 165 170 175 Asn Glu Asp Glu Asp Glu Asp Arg Asp Asp Asn Asp Asp Ser Cys Ala 180 185 190 Gln Lys Lys Gln Arg Val Val Trp Thr Val Glu Leu His Lys Lys Phe 195 200 205 Val Ala Ala Val Asn Gln Leu Gly Tyr Glu Lys Ala Met Pro Lys Lys 210 215 220 Ile Leu Asp Leu Met Asn Val Glu Lys Leu Thr Arg Glu Asn Val Ala 225 230 235 240 Ser His Leu Gln Lys Phe Arg Leu Tyr Leu Lys Arg Ile Ser Gly Val 245 250 255 Ala Asn Gln Gln Ala Ile Met Ala Asn Ser Glu Leu His Phe Met Gln 260 265 270 Met Asn Gly Leu Asp Gly Phe His His Arg Pro Ile Pro Val Gly Ser 275 280 285 Gly Gln Tyr His Gly Gly Ala Pro Ala Met Arg Ser Phe Pro Pro Asn 290 295 300 Gly Ile Leu Gly Arg Leu Asn Ser Ser Ser Gly Ile Gly Val Arg Ser 305 310 315 320 Leu Ser Ser Pro Pro Ala Gly Met Phe Leu Gln Asn Gln Thr Asp Ile 325 330 335 Gly Lys Phe His His Val Ser Ser Leu Pro Leu Asn His Ser Asp Gly 340 345 350 Gly Asn Ile Leu Gln Gly Leu Pro Met Pro Leu Glu Phe Asp Gln Leu 355 360 365 Gln Thr Asn Asn Asn Lys Ser Arg Asn Met Asn Ser Asn Lys Ser Ile 370 375 380 Ala Gly Thr Ser Met Ala Phe Pro Ser Phe Ser Thr Gln Gln Asn Ser 385 390 395 400 Leu Ile Ser Ala Pro Asn Asn Asn Val Val Val Leu Glu Gly His Pro 405 410 415 Gln Ala Thr Pro Pro Gly Phe Pro Gly His Gln Ile Asn Lys Arg Leu 420 425 430 Glu His Trp Ser Asn Ala Val Ser Ser Ser Thr His Pro Pro Pro Pro 435 440 445 Ala His Asn Ser Asn Ser Ile Asn His Gln Phe Asp Val Ser Pro Leu 450 455 460 Pro His Ser Arg Pro Asp Pro Leu Glu Trp Asn Asn Val Ser Ser Ser 465 470 475 480 Tyr Ser Ile Pro Phe Cys Asp Ser Ala Asn Thr Leu Ser Ser Pro Ala 485 490 495 Leu Asp Thr Thr Asn Pro Arg Ala Phe Cys Arg Asn Thr Asp Phe Asp 500 505 510 Ser Asn Thr Asn Val Gln Pro Gly Val Phe Tyr Gly Pro Ser Thr Asp 515 520 525 Ala Met Ala Leu Leu Ser Ser Ser Asn Pro Lys Glu Gly Phe Val Val 530 535 540 Gly Gln Gln Lys Leu Gln Ser Gly Gly Phe Met Val Ala Asp Ala Gly 545 550 555 560 Ser Leu Asp Asp Ile Val Asn Ser Thr Met Lys Gln Val 565 570 11 1016 DNA Arabidopsis thaliana CDS (10)..(858) G1947 11 gttcacaaa atg gat tat aac ctt cca att cca tta gag ggt ctc aaa gaa 51 Met Asp Tyr Asn Leu Pro Ile Pro Leu Glu Gly Leu Lys Glu 1 5 10 acg cca cca acg gct ttc ttg acg aaa aca tac aac ata gtg gag gat 99 Thr Pro Pro Thr Ala Phe Leu Thr Lys Thr Tyr Asn Ile Val Glu Asp 15 20 25 30 tca agc aca aac aac ata gtt tca tgg agc aga gac aac aac agc ttc 147 Ser Ser Thr Asn Asn Ile Val Ser Trp Ser Arg Asp Asn Asn Ser Phe 35 40 45 att gtt tgg gaa cca gag act ttt gcc cta att tgc ctc cct aga tgc 195 Ile Val Trp Glu Pro Glu Thr Phe Ala Leu Ile Cys Leu Pro Arg Cys 50 55 60 ttt aag cac aat aat ttc tcc agc ttt gtt aga cag ctc aat act tat 243 Phe Lys His Asn Asn Phe Ser Ser Phe Val Arg Gln Leu Asn Thr Tyr 65 70 75 ggg ttt aag aag att gat aca gag aga tgg gaa ttt gca aat gag cat 291 Gly Phe Lys Lys Ile Asp Thr Glu Arg Trp Glu Phe Ala Asn Glu His 80 85 90 ttt ctg aag gga gag agg cat ctt ctt aag aac atc aag aga aga aag 339 Phe Leu Lys Gly Glu Arg His Leu Leu Lys Asn Ile Lys Arg Arg Lys 95 100 105 110 aca tca tct caa acg caa acg cag tcg cta gaa gga gag atc cat gag 387 Thr Ser Ser Gln Thr Gln Thr Gln Ser Leu Glu Gly Glu Ile His Glu 115 120 125 ctg cga aga gac aga atg gct tta gaa gta gaa ctg gtt aga ctg cga 435 Leu Arg Arg Asp Arg Met Ala Leu Glu Val Glu Leu Val Arg Leu Arg 130 135 140 cga aaa caa gaa agc gtg aag aca tat ctg cat ttg atg gaa gag aaa 483 Arg Lys Gln Glu Ser Val Lys Thr Tyr Leu His Leu Met Glu Glu Lys 145 150 155 ctg aaa gtc aca gaa gta aag caa gaa atg atg atg aat ttc ttg cta 531 Leu Lys Val Thr Glu Val Lys Gln Glu Met Met Met Asn Phe Leu Leu 160 165 170 aag aag att aag aaa ccg agt ttt tta cag agc tta agg aaa cgt aat 579 Lys Lys Ile Lys Lys Pro Ser Phe Leu Gln Ser Leu Arg Lys Arg Asn 175 180 185 190 ctg caa gga atc aag aat cga gag caa aag caa gag gtg atc tca agc 627 Leu Gln Gly Ile Lys Asn Arg Glu Gln Lys Gln Glu Val Ile Ser Ser 195 200 205 cat ggt gtt gag gat aat gga aag ttt gtt aaa gct gag cca gaa gag 675 His Gly Val Glu Asp Asn Gly Lys Phe Val Lys Ala Glu Pro Glu Glu 210 215 220 tat ggt gat gac atc gat gat caa tgt gga ggt gtg ttt gat tat ggt 723 Tyr Gly Asp Asp Ile Asp Asp Gln Cys Gly Gly Val Phe Asp Tyr Gly 225 230 235 gat gag ctt cac ata gct tca atg gag cat caa gga caa ggg gag gat 771 Asp Glu Leu His Ile Ala Ser Met Glu His Gln Gly Gln Gly Glu Asp 240 245 250 gaa att gaa atg gat agt gaa gga att tgg aag ggt ttc gtg ttg agt 819 Glu Ile Glu Met Asp Ser Glu Gly Ile Trp Lys Gly Phe Val Leu Ser 255 260 265 270 gag gag gag atg tgt gat tta gtg gaa cat ttt ata taa taaactaatg 868 Glu Glu Glu Met Cys Asp Leu Val Glu His Phe Ile 275 280 tattatgaga ggtttttttt tgtttttttg cttttttttt ccgagtttgt catcaagcat 928 tgtatacaat ttgggccaaa ctaaaagccc aacaaaatat ttggccttgg catttgttaa 988 caaattgact aattcggcca caccttcc 1016 12 282 PRT Arabidopsis thaliana 12 Met Asp Tyr Asn Leu Pro Ile Pro Leu Glu Gly Leu Lys Glu Thr Pro 1 5 10 15 Pro Thr Ala Phe Leu Thr Lys Thr Tyr Asn Ile Val Glu Asp Ser Ser 20 25 30 Thr Asn Asn Ile Val Ser Trp Ser Arg Asp Asn Asn Ser Phe Ile Val 35 40 45 Trp Glu Pro Glu Thr Phe Ala Leu Ile Cys Leu Pro Arg Cys Phe Lys 50 55 60 His Asn Asn Phe Ser Ser Phe Val Arg Gln Leu Asn Thr Tyr Gly Phe 65 70 75 80 Lys Lys Ile Asp Thr Glu Arg Trp Glu Phe Ala Asn Glu His Phe Leu 85 90 95 Lys Gly Glu Arg His Leu Leu Lys Asn Ile Lys Arg Arg Lys Thr Ser 100 105 110 Ser Gln Thr Gln Thr Gln Ser Leu Glu Gly Glu Ile His Glu Leu Arg 115 120 125 Arg Asp Arg Met Ala Leu Glu Val Glu Leu Val Arg Leu Arg Arg Lys 130 135 140 Gln Glu Ser Val Lys Thr Tyr Leu His Leu Met Glu Glu Lys Leu Lys 145 150 155 160 Val Thr Glu Val Lys Gln Glu Met Met Met Asn Phe Leu Leu Lys Lys 165 170 175 Ile Lys Lys Pro Ser Phe Leu Gln Ser Leu Arg Lys Arg Asn Leu Gln 180 185 190 Gly Ile Lys Asn Arg Glu Gln Lys Gln Glu Val Ile Ser Ser His Gly 195 200 205 Val Glu Asp Asn Gly Lys Phe Val Lys Ala Glu Pro Glu Glu Tyr Gly 210 215 220 Asp Asp Ile Asp Asp Gln Cys Gly Gly Val Phe Asp Tyr Gly Asp Glu 225 230 235 240 Leu His Ile Ala Ser Met Glu His Gln Gly Gln Gly Glu Asp Glu Ile 245 250 255 Glu Met Asp Ser Glu Gly Ile Trp Lys Gly Phe Val Leu Ser Glu Glu 260 265 270 Glu Met Cys Asp Leu Val Glu His Phe Ile 275 280 13 959 DNA Arabidopsis thaliana CDS (50)..(733) G152 13 cctagaacgc accaagatct aaaggaagat caaaataggg tttaaatta atg ggg aga 58 Met Gly Arg 1 ggg aag att gtg atc cag aag atc gat gat tcc acg agt aga caa gtc 106 Gly Lys Ile Val Ile Gln Lys Ile Asp Asp Ser Thr Ser Arg Gln Val 5 10 15 act ttc tcc aaa aga aga aag ggt ctc atc aag aaa gct aaa gaa ctt 154 Thr Phe Ser Lys Arg Arg Lys Gly Leu Ile Lys Lys Ala Lys Glu Leu 20 25 30 35 gct att ctc tgc gac gcc gag gtc tgt ctc atc att ttc tcc aac act 202 Ala Ile Leu Cys Asp Ala Glu Val Cys Leu Ile Ile Phe Ser Asn Thr 40 45 50 gac aag ctc tat gac ttt gcc agc tcc agt gtg aaa tct act att gaa 250 Asp Lys Leu Tyr Asp Phe Ala Ser Ser Ser Val Lys Ser Thr Ile Glu 55 60 65 cga ttc aat acg gct aag atg gag gag caa gaa cta atg aac cct gca 298 Arg Phe Asn Thr Ala Lys Met Glu Glu Gln Glu Leu Met Asn Pro Ala 70 75 80 tca gaa gtt aag ttt tgg cag aga gag gct gaa act cta agg caa gaa 346 Ser Glu Val Lys Phe Trp Gln Arg Glu Ala Glu Thr Leu Arg Gln Glu 85 90 95 ttg cac tca ttg caa gaa aat tat cgg caa cta acg gga gtg gaa tta 394 Leu His Ser Leu Gln Glu Asn Tyr Arg Gln Leu Thr Gly Val Glu Leu 100 105 110 115 aat ggt ttg agc gtt aag gag tta caa aac ata gag agt caa ctt gaa 442 Asn Gly Leu Ser Val Lys Glu Leu Gln Asn Ile Glu Ser Gln Leu Glu 120 125 130 atg agt tta cgt gga att cgt atg aaa agg gaa caa att ttg acc aat 490 Met Ser Leu Arg Gly Ile Arg Met Lys Arg Glu Gln Ile Leu Thr Asn 135 140 145 gaa att aaa gag cta acc aga aag agg aat ctt gtt cat cat gaa aac 538 Glu Ile Lys Glu Leu Thr Arg Lys Arg Asn Leu Val His His Glu Asn 150 155 160 ctc gaa ttg tcg aga aaa gta caa agg att cat caa gaa aat gtc gaa 586 Leu Glu Leu Ser Arg Lys Val Gln Arg Ile His Gln Glu Asn Val Glu 165 170 175 cta tac aag aag gct tat gga acg tcg aac aca aat gga ttg gga cat 634 Leu Tyr Lys Lys Ala Tyr Gly Thr Ser Asn Thr Asn Gly Leu Gly His 180 185 190 195 cat gag cta gta gat gca gtt tat gaa tcc cat gca cag gtt agg ctg 682 His Glu Leu Val Asp Ala Val Tyr Glu Ser His Ala Gln Val Arg Leu 200 205 210 cag cta agc cag cct gag cag tcc cat tat aag aca tct tca aac agc 730 Gln Leu Ser Gln Pro Glu Gln Ser His Tyr Lys Thr Ser Ser Asn Ser 215 220 225 taa gatcatataa gagatatata acaaattgtt cgttcttgat tatctcaaaa 783 ccctttcaaa tatatatacg tgcatattat atatgaagac tcgtttgact atgtcaatat 843 atatgttttc atgcaggagt aagtgtgagt gtaatcatgt cggagagcaa accaaaggtt 903 tgatttgtac gatatatact tatatatggt ctcaagtgaa agcaatggaa cagctt 959 14 227 PRT Arabidopsis thaliana 14 Met Gly Arg Gly Lys Ile Val Ile Gln Lys Ile Asp Asp Ser Thr Ser 1 5 10 15 Arg Gln Val Thr Phe Ser Lys Arg Arg Lys Gly Leu Ile Lys Lys Ala 20 25 30 Lys Glu Leu Ala Ile Leu Cys Asp Ala Glu Val Cys Leu Ile Ile Phe 35 40 45 Ser Asn Thr Asp Lys Leu Tyr Asp Phe Ala Ser Ser Ser Val Lys Ser 50 55 60 Thr Ile Glu Arg Phe Asn Thr Ala Lys Met Glu Glu Gln Glu Leu Met 65 70 75 80 Asn Pro Ala Ser Glu Val Lys Phe Trp Gln Arg Glu Ala Glu Thr Leu 85 90 95 Arg Gln Glu Leu His Ser Leu Gln Glu Asn Tyr Arg Gln Leu Thr Gly 100 105 110 Val Glu Leu Asn Gly Leu Ser Val Lys Glu Leu Gln Asn Ile Glu Ser 115 120 125 Gln Leu Glu Met Ser Leu Arg Gly Ile Arg Met Lys Arg Glu Gln Ile 130 135 140 Leu Thr Asn Glu Ile Lys Glu Leu Thr Arg Lys Arg Asn Leu Val His 145 150 155 160 His Glu Asn Leu Glu Leu Ser Arg Lys Val Gln Arg Ile His Gln Glu 165 170 175 Asn Val Glu Leu Tyr Lys Lys Ala Tyr Gly Thr Ser Asn Thr Asn Gly 180 185 190 Leu Gly His His Glu Leu Val Asp Ala Val Tyr Glu Ser His Ala Gln 195 200 205 Val Arg Leu Gln Leu Ser Gln Pro Glu Gln Ser His Tyr Lys Thr Ser 210 215 220 Ser Asn Ser 225 15 1098 DNA Arabidopsis thaliana CDS (97)..(801) G153 15 aaaaaaaaga agcttctcct cttcctctgc cttcttcttt ccatttattg caaaccctga 60 tcaattggtt ttggtgttag tcttttgggg agagag atg ggg aga ggg aag ata 114 Met Gly Arg Gly Lys Ile 1 5 gtt ata cga agg atc gat aac tct aca agt aga caa gtg act ttc tcc 162 Val Ile Arg Arg Ile Asp Asn Ser Thr Ser Arg Gln Val Thr Phe Ser 10 15 20 aag aga agg agt ggt ttg ctt aag aag gct aaa gag tta tcg atc ctt 210 Lys Arg Arg Ser Gly Leu Leu Lys Lys Ala Lys Glu Leu Ser Ile Leu 25 30 35 tgt gat gca gaa gtt ggt gtt atc ata ttc tct agc acc gga aag ctc 258 Cys Asp Ala Glu Val Gly Val Ile Ile Phe Ser Ser Thr Gly Lys Leu 40 45 50 tac gac tac gca agc aat tca agt atg aaa aca atc att gag cgg tac 306 Tyr Asp Tyr Ala Ser Asn Ser Ser Met Lys Thr Ile Ile Glu Arg Tyr 55 60 65 70 aac aga gta aaa gag gag cag cat caa ctt ctg aat cat gcc tca gag 354 Asn Arg Val Lys Glu Glu Gln His Gln Leu Leu Asn His Ala Ser Glu 75 80 85 ata aag ttt tgg caa aga gag gtt gca agt ttg cag cag cag ctc caa 402 Ile Lys Phe Trp Gln Arg Glu Val Ala Ser Leu Gln Gln Gln Leu Gln 90 95 100 cat cta caa gaa tgc cac agg aaa cta gtg gga gag gaa ctt tct gga 450 His Leu Gln Glu Cys His Arg Lys Leu Val Gly Glu Glu Leu Ser Gly 105 110 115 atg aat gct aac gac cta caa aat ctt gaa gac cag cta gta aca agt 498 Met Asn Ala Asn Asp Leu Gln Asn Leu Glu Asp Gln Leu Val Thr Ser 120 125 130 cta aaa ggt gtt cgt ctc aaa aag gat caa ctt atg aca aat gaa atc 546 Leu Lys Gly Val Arg Leu Lys Lys Asp Gln Leu Met Thr Asn Glu Ile 135 140 145 150 aga gaa ctt aat cgt aag gga caa atc atc caa aaa gag aat cac gag 594 Arg Glu Leu Asn Arg Lys Gly Gln Ile Ile Gln Lys Glu Asn His Glu 155 160 165 cta caa aat att gta gat ata atg cgt aag gaa aat att aaa ttg caa 642 Leu Gln Asn Ile Val Asp Ile Met Arg Lys Glu Asn Ile Lys Leu Gln 170 175 180 aag aag gtt cat gga aga aca aat gtg att gaa ggc aat tca agt gta 690 Lys Lys Val His Gly Arg Thr Asn Val Ile Glu Gly Asn Ser Ser Val 185 190 195 gat cca ata agc aat gga acc aca aca tat gca cca ccg caa ctt caa 738 Asp Pro Ile Ser Asn Gly Thr Thr Thr Tyr Ala Pro Pro Gln Leu Gln 200 205 210 ctc ata caa cta caa cca gct cct aga gaa aaa tca atc aga cta ggg 786 Leu Ile Gln Leu Gln Pro Ala Pro Arg Glu Lys Ser Ile Arg Leu Gly 215 220 225 230 cta caa ctt tcc tag caaaacatgt gggacatcga acaatatacg aaaagagttt 841 Leu Gln Leu Ser gtatgtcatc ttcagtaaca accaagctgg atcatttcat tcttggttat gtaattctgt 901 ttactacttt ggagtttaat atgttatatg acaagtttct ctttgtcaag ttacttgtgt 961 atgtacatca taaaataatg atgtgatgtg agtgccgaac atactagaca tcattttacc 1021 gtgtgttttt ttcgggtaca ttaaatgtac aaaatccagt ctaattggca tttttataca 1081 aaaaaaaaaa aaaaaaa 1098 16 234 PRT Arabidopsis thaliana 16 Met Gly Arg Gly Lys Ile Val Ile Arg Arg Ile Asp Asn Ser Thr Ser 1 5 10 15 Arg Gln Val Thr Phe Ser Lys Arg Arg Ser Gly Leu Leu Lys Lys Ala 20 25 30 Lys Glu Leu Ser Ile Leu Cys Asp Ala Glu Val Gly Val Ile Ile Phe 35 40 45 Ser Ser Thr Gly Lys Leu Tyr Asp Tyr Ala Ser Asn Ser Ser Met Lys 50 55 60 Thr Ile Ile Glu Arg Tyr Asn Arg Val Lys Glu Glu Gln His Gln Leu 65 70 75 80 Leu Asn His Ala Ser Glu Ile Lys Phe Trp Gln Arg Glu Val Ala Ser 85 90 95 Leu Gln Gln Gln Leu Gln His Leu Gln Glu Cys His Arg Lys Leu Val 100 105 110 Gly Glu Glu Leu Ser Gly Met Asn Ala Asn Asp Leu Gln Asn Leu Glu 115 120 125 Asp Gln Leu Val Thr Ser Leu Lys Gly Val Arg Leu Lys Lys Asp Gln 130 135 140 Leu Met Thr Asn Glu Ile Arg Glu Leu Asn Arg Lys Gly Gln Ile Ile 145 150 155 160 Gln Lys Glu Asn His Glu Leu Gln Asn Ile Val Asp Ile Met Arg Lys 165 170 175 Glu Asn Ile Lys Leu Gln Lys Lys Val His Gly Arg Thr Asn Val Ile 180 185 190 Glu Gly Asn Ser Ser Val Asp Pro Ile Ser Asn Gly Thr Thr Thr Tyr 195 200 205 Ala Pro Pro Gln Leu Gln Leu Ile Gln Leu Gln Pro Ala Pro Arg Glu 210 215 220 Lys Ser Ile Arg Leu Gly Leu Gln Leu Ser 225 230 17 1210 DNA Arabidopsis thaliana CDS (117)..(839) G860 17 acaaaaccac atctctgaac tgaaccaatt tctcttctcc cccttccggt tatcggatta 60 ccagatctcg tttcccgcga tctagtttat tctttgaaaa agtgatagaa gcagaa atg 119 Met 1 gga agg ggc aag atc gcg att aag agg atc aat aac tct acg agc cgt 167 Gly Arg Gly Lys Ile Ala Ile Lys Arg Ile Asn Asn Ser Thr Ser Arg 5 10 15 cag gtt acg ttc tcg aag cga agg aat gga ttg ttg aag aaa gct aag 215 Gln Val Thr Phe Ser Lys Arg Arg Asn Gly Leu Leu Lys Lys Ala Lys 20 25 30 gag ctt gcg att ctc tgc gat gct gag gtt ggt gtc atc atc ttc tcc 263 Glu Leu Ala Ile Leu Cys Asp Ala Glu Val Gly Val Ile Ile Phe Ser 35 40 45 agc acc ggt agg ctc tac gat ttc tcc agc tcc agc atg aaa tcg gtc 311 Ser Thr Gly Arg Leu Tyr Asp Phe Ser Ser Ser Ser Met Lys Ser Val 50 55 60 65 ata gag aga tac agc gat gcc aaa gga gaa acc agt tca gaa aat gat 359 Ile Glu Arg Tyr Ser Asp Ala Lys Gly Glu Thr Ser Ser Glu Asn Asp 70 75 80 ccc gct tca gaa att cag ttc tgg caa aag gag gct gcg att cta aag 407 Pro Ala Ser Glu Ile Gln Phe Trp Gln Lys Glu Ala Ala Ile Leu Lys 85 90 95 cgt cag cta cat aac ttg caa gaa aac cac cgg caa atg atg ggg gag 455 Arg Gln Leu His Asn Leu Gln Glu Asn His Arg Gln Met Met Gly Glu 100 105 110 gag ctc tct gga cta agt gta gaa gct tta cag aat ttg gaa aat cag 503 Glu Leu Ser Gly Leu Ser Val Glu Ala Leu Gln Asn Leu Glu Asn Gln 115 120 125 ctt gaa ttg agc ctt cgt ggc gtt cga atg aaa aag gat caa atg tta 551 Leu Glu Leu Ser Leu Arg Gly Val Arg Met Lys Lys Asp Gln Met Leu 130 135 140 145 atc gaa gaa ata caa gta ctt aac cga gag ggg aat ctc gtt cac caa 599 Ile Glu Glu Ile Gln Val Leu Asn Arg Glu Gly Asn Leu Val His Gln 150 155 160 gag aat tta gac ctc cac aag aaa gta aac cta atg cac caa cag aac 647 Glu Asn Leu Asp Leu His Lys Lys Val Asn Leu Met His Gln Gln Asn 165 170 175 atg gaa cta cat gaa aag gtt tca gag gtc gag ggt gtg aaa atc gca 695 Met Glu Leu His Glu Lys Val Ser Glu Val Glu Gly Val Lys Ile Ala 180 185 190 aac aag aat tct ctt ctc aca aat ggt cta gac atg aga gat acc tcg 743 Asn Lys Asn Ser Leu Leu Thr Asn Gly Leu Asp Met Arg Asp Thr Ser 195 200 205 aac gaa cat gtc cat ctt cag ctc agc caa ccg cag cat gat cat gag 791 Asn Glu His Val His Leu Gln Leu Ser Gln Pro Gln His Asp His Glu 210 215 220 225 acg cat tca aaa gct atc caa ctc aac tat ttt tcc ttc att gca taa 839 Thr His Ser Lys Ala Ile Gln Leu Asn Tyr Phe Ser Phe Ile Ala 230 235 240 tataattcgg tgtgccaaca cacttatgtt gacctcgtcg gaatcatatc acaattcact 899 gtgtcagctt gcctctgcat aagcgaaaat aaaaacataa acatgatcag tttgcattcc 959 atatctatca aacaccagct ttgtaacttt taaaactttt tctccgtgca aagacctttg 1019 gtttggcgct taagcatgta gtttgatgat caaaggaaat gggtgtttta gcataaagtt 1079 gtcacccttc cgttgcattt tagcttccca tccaaatcaa tttgtaaaat gtgagttagt 1139 ttgcagcatg aaagctgatt aaatatcagt cccgttatca caagaggtaa aaaannnaaa 1199 aaaaaaaaaa a 1210 18 240 PRT Arabidopsis thaliana 18 Met Gly Arg Gly Lys Ile Ala Ile Lys Arg Ile Asn Asn Ser Thr Ser 1 5 10 15 Arg Gln Val Thr Phe Ser Lys Arg Arg Asn Gly Leu Leu Lys Lys Ala 20 25 30 Lys Glu Leu Ala Ile Leu Cys Asp Ala Glu Val Gly Val Ile Ile Phe 35 40 45 Ser Ser Thr Gly Arg Leu Tyr Asp Phe Ser Ser Ser Ser Met Lys Ser 50 55 60 Val Ile Glu Arg Tyr Ser Asp Ala Lys Gly Glu Thr Ser Ser Glu Asn 65 70 75 80 Asp Pro Ala Ser Glu Ile Gln Phe Trp Gln Lys Glu Ala Ala Ile Leu 85 90 95 Lys Arg Gln Leu His Asn Leu Gln Glu Asn His Arg Gln Met Met Gly 100 105 110 Glu Glu Leu Ser Gly Leu Ser Val Glu Ala Leu Gln Asn Leu Glu Asn 115 120 125 Gln Leu Glu Leu Ser Leu Arg Gly Val Arg Met Lys Lys Asp Gln Met 130 135 140 Leu Ile Glu Glu Ile Gln Val Leu Asn Arg Glu Gly Asn Leu Val His 145 150 155 160 Gln Glu Asn Leu Asp Leu His Lys Lys Val Asn Leu Met His Gln Gln 165 170 175 Asn Met Glu Leu His Glu Lys Val Ser Glu Val Glu Gly Val Lys Ile 180 185 190 Ala Asn Lys Asn Ser Leu Leu Thr Asn Gly Leu Asp Met Arg Asp Thr 195 200 205 Ser Asn Glu His Val His Leu Gln Leu Ser Gln Pro Gln His Asp His 210 215 220 Glu Thr His Ser Lys Ala Ile Gln Leu Asn Tyr Phe Ser Phe Ile Ala 225 230 235 240 19 850 DNA Arabidopsis thaliana CDS (81)..(494) G2347 19 agcccatcct tcaacattgc ttcctaacca gaaatccacc atcatcttcc cacgaataca 60 acttaaagct ttaccagaaa atg gag ggt cag aga aca caa cgc cgg ggt tac 113 Met Glu Gly Gln Arg Thr Gln Arg Arg Gly Tyr 1 5 10 ttg aaa gac aag gct aca gtc tcc aac ctt gtt gaa gaa gaa atg gag 161 Leu Lys Asp Lys Ala Thr Val Ser Asn Leu Val Glu Glu Glu Met Glu 15 20 25 aat ggc atg gat gga gaa gag gag gat gga gga gac gaa gac aaa agg 209 Asn Gly Met Asp Gly Glu Glu Glu Asp Gly Gly Asp Glu Asp Lys Arg 30 35 40 aag aag gtg atg gaa aga gtt aga ggt cct agc act gac cgt gtt cca 257 Lys Lys Val Met Glu Arg Val Arg Gly Pro Ser Thr Asp Arg Val Pro 45 50 55 tcg cga ctg tgc cag gtc gat agg tgc act gtt aat ttg act gag gcc 305 Ser Arg Leu Cys Gln Val Asp Arg Cys Thr Val Asn Leu Thr Glu Ala 60 65 70 75 aag cag tat tac cgc aga cac aga gta tgt gaa gta cat gca aag gca 353 Lys Gln Tyr Tyr Arg Arg His Arg Val Cys Glu Val His Ala Lys Ala 80 85 90 tct gct gcg act gtt gca ggg gtc agg caa cgc ttt tgt caa caa tgc 401 Ser Ala Ala Thr Val Ala Gly Val Arg Gln Arg Phe Cys Gln Gln Cys 95 100 105 agc agg ttt cat gag cta cca gag ttt gat gaa gct aaa aga agc tgc 449 Ser Arg Phe His Glu Leu Pro Glu Phe Asp Glu Ala Lys Arg Ser Cys 110 115 120 agg agg cgc tta gct gga cac aat gag agg agg agg aag atc tct 494 Arg Arg Arg Leu Ala Gly His Asn Glu Arg Arg Arg Lys Ile Ser 125 130 135 ggtgacagtt ttggagaagg gtcaggccgg agagggttta gcggtcaact gatccagact 554 caagaaagaa acagggtaga caggaaactt cctatgacca actcatcatt caagcgacca 614 cagatcagat aaaccctccc gctctctctc ttctgtcatc tacatatgct ctatctacac 674 tcttattaga caaataatgg catctaacaa tgtcaagaaa agttggtcat ggtattaaat 734 cctacacgga tatataacta taaacctcta gtcccctcta tgctgtcctg taatgaatat 794 ctatccggaa atgtattcgc atagtcttgc gtctaataat gtttattgat tttgta 850 20 138 PRT Arabidopsis thaliana 20 Met Glu Gly Gln Arg Thr Gln Arg Arg Gly Tyr Leu Lys Asp Lys Ala 1 5 10 15 Thr Val Ser Asn Leu Val Glu Glu Glu Met Glu Asn Gly Met Asp Gly 20 25 30 Glu Glu Glu Asp Gly Gly Asp Glu Asp Lys Arg Lys Lys Val Met Glu 35 40 45 Arg Val Arg Gly Pro Ser Thr Asp Arg Val Pro Ser Arg Leu Cys Gln 50 55 60 Val Asp Arg Cys Thr Val Asn Leu Thr Glu Ala Lys Gln Tyr Tyr Arg 65 70 75 80 Arg His Arg Val Cys Glu Val His Ala Lys Ala Ser Ala Ala Thr Val 85 90 95 Ala Gly Val Arg Gln Arg Phe Cys Gln Gln Cys Ser Arg Phe His Glu 100 105 110 Leu Pro Glu Phe Asp Glu Ala Lys Arg Ser Cys Arg Arg Arg Leu Ala 115 120 125 Gly His Asn Glu Arg Arg Arg Lys Ile Ser 130 135 21 1882 DNA Arabidopsis thaliana CDS (87)..(1745) G722 21 atacaacttt ttgtctcttt ctctactaat aataataatc cgaactttgt ttgttcttct 60 acttcaattc ataatctttg acggcg atg act atg gag caa gaa att gaa gtc 113 Met Thr Met Glu Gln Glu Ile Glu Val 1 5 ttg gac cag ttt ccg gtt ggg atg aga gtt ctt gct gtt gac gat gac 161 Leu Asp Gln Phe Pro Val Gly Met Arg Val Leu Ala Val Asp Asp Asp 10 15 20 25 cag act tgt ctc cgt att ctc cag act ttg ctt cag cgc tgc caa tat 209 Gln Thr Cys Leu Arg Ile Leu Gln Thr Leu Leu Gln Arg Cys Gln Tyr 30 35 40 cac gtt aca aca acg aat cag gca cag acc gca ttg gag ttg ttg agg 257 His Val Thr Thr Thr Asn Gln Ala Gln Thr Ala Leu Glu Leu Leu Arg 45 50 55 gag aac aag aat aag ttt gat ctt gtt att agc gat gtc gac atg cca 305 Glu Asn Lys Asn Lys Phe Asp Leu Val Ile Ser Asp Val Asp Met Pro 60 65 70 gac atg gat ggt ttc aag ctg ctt gag ctt gtt ggt ctt gaa atg gac 353 Asp Met Asp Gly Phe Lys Leu Leu Glu Leu Val Gly Leu Glu Met Asp 75 80 85 tta cct gtc ata atg tta tct gcg cat agc gat cca aag tat gtg atg 401 Leu Pro Val Ile Met Leu Ser Ala His Ser Asp Pro Lys Tyr Val Met 90 95 100 105 aaa gga gtc aag cac ggt gcc tgt gat tat ctg ctt aaa ccg gtt cga 449 Lys Gly Val Lys His Gly Ala Cys Asp Tyr Leu Leu Lys Pro Val Arg 110 115 120 att gag gag ctt aag aac ata tgg caa cat gtt gtg aga aag agc aaa 497 Ile Glu Glu Leu Lys Asn Ile Trp Gln His Val Val Arg Lys Ser Lys 125 130 135 ctt aag aag aat aag agc aat gtg agt aat ggt tca gga aac tgt gat 545 Leu Lys Lys Asn Lys Ser Asn Val Ser Asn Gly Ser Gly Asn Cys Asp 140 145 150 aaa gca aac aga aaa cgt aaa gaa cag tat gaa gag gag gaa gag gaa 593 Lys Ala Asn Arg Lys Arg Lys Glu Gln Tyr Glu Glu Glu Glu Glu Glu 155 160 165 gaa aga ggg aat gat aat gat gat cca acg gcg cag aag aag cct cgt 641 Glu Arg Gly Asn Asp Asn Asp Asp Pro Thr Ala Gln Lys Lys Pro Arg 170 175 180 185 gtt ctt tgg acg cat gag ctg cac aat aaa ttc cta gca gct gtt gat 689 Val Leu Trp Thr His Glu Leu His Asn Lys Phe Leu Ala Ala Val Asp 190 195 200 cat tta ggc gtt gag aga gct gtt cca aaa aag att cta gat ctg atg 737 His Leu Gly Val Glu Arg Ala Val Pro Lys Lys Ile Leu Asp Leu Met 205 210 215 aat gtt gac aaa ctc act aga gag aat gtt gca agc cac ctt cag aaa 785 Asn Val Asp Lys Leu Thr Arg Glu Asn Val Ala Ser His Leu Gln Lys 220 225 230 ttc cgc gtt gct ctg aag aag gtg tct gat gac gcc att caa caa gct 833 Phe Arg Val Ala Leu Lys Lys Val Ser Asp Asp Ala Ile Gln Gln Ala 235 240 245 aac agg gcg gct att gac tca cat ttt atg caa atg aat tct cag aaa 881 Asn Arg Ala Ala Ile Asp Ser His Phe Met Gln Met Asn Ser Gln Lys 250 255 260 265 gga ctt ggt ggc ttc tac cac cac cac cgc gga ata cct gtt gga tcc 929 Gly Leu Gly Gly Phe Tyr His His His Arg Gly Ile Pro Val Gly Ser 270 275 280 ggt cag ttc cat ggt gga acc aca atg atg agg cat tac tct tca aat 977 Gly Gln Phe His Gly Gly Thr Thr Met Met Arg His Tyr Ser Ser Asn 285 290 295 agg aat ctt ggt cgt ctg aat tcc ctt gga gca gga atg ttc caa cca 1025 Arg Asn Leu Gly Arg Leu Asn Ser Leu Gly Ala Gly Met Phe Gln Pro 300 305 310 gtc tca tca tcg ttt cct cgt aac cat aat gat gga gga aac ata ctt 1073 Val Ser Ser Ser Phe Pro Arg Asn His Asn Asp Gly Gly Asn Ile Leu 315 320 325 cag ggt ttg ccg cta gaa gag ctt cag atc aac aac aac atc aac agg 1121 Gln Gly Leu Pro Leu Glu Glu Leu Gln Ile Asn Asn Asn Ile Asn Arg 330 335 340 345 gct ttt cca agc ttt act tca caa caa aac tct cca atg gta gct ccc 1169 Ala Phe Pro Ser Phe Thr Ser Gln Gln Asn Ser Pro Met Val Ala Pro 350 355 360 agt aat ctg tta ctt ctc gag ggt aac ccg cag tca tca tct tta ccc 1217 Ser Asn Leu Leu Leu Leu Glu Gly Asn Pro Gln Ser Ser Ser Leu Pro 365 370 375 tca aac ccg ggt ttt tct cct cat ttc gag atc agc aag cgt cta gaa 1265 Ser Asn Pro Gly Phe Ser Pro His Phe Glu Ile Ser Lys Arg Leu Glu 380 385 390 cat tgg tca aac gct gca ttg tca acc aac att cca cag agt gat gtt 1313 His Trp Ser Asn Ala Ala Leu Ser Thr Asn Ile Pro Gln Ser Asp Val 395 400 405 cat tca aaa cct gac acc ttg gaa tgg aat gcg ttc tgc gac tca gct 1361 His Ser Lys Pro Asp Thr Leu Glu Trp Asn Ala Phe Cys Asp Ser Ala 410 415 420 425 agt ccg cta gta aac cca aac ctg gat aca aat ccg gca tct ctc tgc 1409 Ser Pro Leu Val Asn Pro Asn Leu Asp Thr Asn Pro Ala Ser Leu Cys 430 435 440 aga aac acg ggt ttt gga tcc aca aat gct gca caa aca gac ttc ttt 1457 Arg Asn Thr Gly Phe Gly Ser Thr Asn Ala Ala Gln Thr Asp Phe Phe 445 450 455 tat cca tta cag atg aat cag cag cct gca aac aac tca ggt cca gtg 1505 Tyr Pro Leu Gln Met Asn Gln Gln Pro Ala Asn Asn Ser Gly Pro Val 460 465 470 aca gaa gct caa ctg ttt aga agt agc aat cca aac gaa ggt tta ctc 1553 Thr Glu Ala Gln Leu Phe Arg Ser Ser Asn Pro Asn Glu Gly Leu Leu 475 480 485 atg gga caa cag aag ctt cag agt ggt ttg atg gct tct gat gct ggt 1601 Met Gly Gln Gln Lys Leu Gln Ser Gly Leu Met Ala Ser Asp Ala Gly 490 495 500 505 tcc tta gat gat ata gtc aat tcc tta atg aca cag gaa cag agc caa 1649 Ser Leu Asp Asp Ile Val Asn Ser Leu Met Thr Gln Glu Gln Ser Gln 510 515 520 tct gat ttc tcg gaa ggt gat tgg gat ttg gat ggt tta gct cac tcg 1697 Ser Asp Phe Ser Glu Gly Asp Trp Asp Leu Asp Gly Leu Ala His Ser 525 530 535 gaa cat gca tac gag aaa ctc cat ttt ccc ttt tct ttg tca gct tga 1745 Glu His Ala Tyr Glu Lys Leu His Phe Pro Phe Ser Leu Ser Ala 540 545 550 gaaacctgtt ttattcagac acaatcaatt attattatct tttggttctg tctcttctct 1805 cttctctgta atgaaagtgt aagctattgt ttaccgctcc cccactggtt tgagcaactt 1865 aggaagatcc aaatcca 1882 22 552 PRT Arabidopsis thaliana 22 Met Thr Met Glu Gln Glu Ile Glu Val Leu Asp Gln Phe Pro Val Gly 1 5 10 15 Met Arg Val Leu Ala Val Asp Asp Asp Gln Thr Cys Leu Arg Ile Leu 20 25 30 Gln Thr Leu Leu Gln Arg Cys Gln Tyr His Val Thr Thr Thr Asn Gln 35 40 45 Ala Gln Thr Ala Leu Glu Leu Leu Arg Glu Asn Lys Asn Lys Phe Asp 50 55 60 Leu Val Ile Ser Asp Val Asp Met Pro Asp Met Asp Gly Phe Lys Leu 65 70 75 80 Leu Glu Leu Val Gly Leu Glu Met Asp Leu Pro Val Ile Met Leu Ser 85 90 95 Ala His Ser Asp Pro Lys Tyr Val Met Lys Gly Val Lys His Gly Ala 100 105 110 Cys Asp Tyr Leu Leu Lys Pro Val Arg Ile Glu Glu Leu Lys Asn Ile 115 120 125 Trp Gln His Val Val Arg Lys Ser Lys Leu Lys Lys Asn Lys Ser Asn 130 135 140 Val Ser Asn Gly Ser Gly Asn Cys Asp Lys Ala Asn Arg Lys Arg Lys 145 150 155 160 Glu Gln Tyr Glu Glu Glu Glu Glu Glu Glu Arg Gly Asn Asp Asn Asp 165 170 175 Asp Pro Thr Ala Gln Lys Lys Pro Arg Val Leu Trp Thr His Glu Leu 180 185 190 His Asn Lys Phe Leu Ala Ala Val Asp His Leu Gly Val Glu Arg Ala 195 200 205 Val Pro Lys Lys Ile Leu Asp Leu Met Asn Val Asp Lys Leu Thr Arg 210 215 220 Glu Asn Val Ala Ser His Leu Gln Lys Phe Arg Val Ala Leu Lys Lys 225 230 235 240 Val Ser Asp Asp Ala Ile Gln Gln Ala Asn Arg Ala Ala Ile Asp Ser 245 250 255 His Phe Met Gln Met Asn Ser Gln Lys Gly Leu Gly Gly Phe Tyr His 260 265 270 His His Arg Gly Ile Pro Val Gly Ser Gly Gln Phe His Gly Gly Thr 275 280 285 Thr Met Met Arg His Tyr Ser Ser Asn Arg Asn Leu Gly Arg Leu Asn 290 295 300 Ser Leu Gly Ala Gly Met Phe Gln Pro Val Ser Ser Ser Phe Pro Arg 305 310 315 320 Asn His Asn Asp Gly Gly Asn Ile Leu Gln Gly Leu Pro Leu Glu Glu 325 330 335 Leu Gln Ile Asn Asn Asn Ile Asn Arg Ala Phe Pro Ser Phe Thr Ser 340 345 350 Gln Gln Asn Ser Pro Met Val Ala Pro Ser Asn Leu Leu Leu Leu Glu 355 360 365 Gly Asn Pro Gln Ser Ser Ser Leu Pro Ser Asn Pro Gly Phe Ser Pro 370 375 380 His Phe Glu Ile Ser Lys Arg Leu Glu His Trp Ser Asn Ala Ala Leu 385 390 395 400 Ser Thr Asn Ile Pro Gln Ser Asp Val His Ser Lys Pro Asp Thr Leu 405 410 415 Glu Trp Asn Ala Phe Cys Asp Ser Ala Ser Pro Leu Val Asn Pro Asn 420 425 430 Leu Asp Thr Asn Pro Ala Ser Leu Cys Arg Asn Thr Gly Phe Gly Ser 435 440 445 Thr Asn Ala Ala Gln Thr Asp Phe Phe Tyr Pro Leu Gln Met Asn Gln 450 455 460 Gln Pro Ala Asn Asn Ser Gly Pro Val Thr Glu Ala Gln Leu Phe Arg 465 470 475 480 Ser Ser Asn Pro Asn Glu Gly Leu Leu Met Gly Gln Gln Lys Leu Gln 485 490 495 Ser Gly Leu Met Ala Ser Asp Ala Gly Ser Leu Asp Asp Ile Val Asn 500 505 510 Ser Leu Met Thr Gln Glu Gln Ser Gln Ser Asp Phe Ser Glu Gly Asp 515 520 525 Trp Asp Leu Asp Gly Leu Ala His Ser Glu His Ala Tyr Glu Lys Leu 530 535 540 His Phe Pro Phe Ser Leu Ser Ala 545 550 23 2010 DNA Arabidopsis thaliana CDS (1)..(2010) G1493 23 atg atg aat ccg agt cac gga aga gga ctc gga tcg gct ggt ggg tcc 48 Met Met Asn Pro Ser His Gly Arg Gly Leu Gly Ser Ala Gly Gly Ser 1 5 10 15 agc tcc ggt aga aat caa gga ggt ggt ggt gag acc gtc gtc gag atg 96 Ser Ser Gly Arg Asn Gln Gly Gly Gly Gly Glu Thr Val Val Glu Met 20 25 30 ttt cct tct ggt ctt cga gtt ctt gtc gtt gac gat gac cca act tgt 144 Phe Pro Ser Gly Leu Arg Val Leu Val Val Asp Asp Asp Pro Thr Cys 35 40 45 ctc atg atc tta gag agg atg ctt agg act tgt ctt tac gaa gta acg 192 Leu Met Ile Leu Glu Arg Met Leu Arg Thr Cys Leu Tyr Glu Val Thr 50 55 60 aaa tgc aac aga gca gag atg gca ttg tct ctg ctc cgg aag aac aaa 240 Lys Cys Asn Arg Ala Glu Met Ala Leu Ser Leu Leu Arg Lys Asn Lys 65 70 75 80 cat gga ttc gat ata gta atc agt gat gtt cat atg cct gac atg gac 288 His Gly Phe Asp Ile Val Ile Ser Asp Val His Met Pro Asp Met Asp 85 90 95 ggt ttc aag ctt ctt gag cat gtt ggt cta gag atg gac tta cct gtt 336 Gly Phe Lys Leu Leu Glu His Val Gly Leu Glu Met Asp Leu Pro Val 100 105 110 atc atg atg tct gcg gat gat tca aag agt gtg gtt cta aag gga gta 384 Ile Met Met Ser Ala Asp Asp Ser Lys Ser Val Val Leu Lys Gly Val 115 120 125 acg cac ggt gcg gtt gat tac ctt atc aag cct gta cgt atg gag gca 432 Thr His Gly Ala Val Asp Tyr Leu Ile Lys Pro Val Arg Met Glu Ala 130 135 140 ctt aag aac ata tgg cag cat gta gtt agg aag agg aga agt gaa tgg 480 Leu Lys Asn Ile Trp Gln His Val Val Arg Lys Arg Arg Ser Glu Trp 145 150 155 160 agt gta ccg gaa cat tct ggg agc att gag gag act ggc gag aga cag 528 Ser Val Pro Glu His Ser Gly Ser Ile Glu Glu Thr Gly Glu Arg Gln 165 170 175 cag cag caa cat aga gga ggt ggt ggt ggt gca gct gtt tct ggt gga 576 Gln Gln Gln His Arg Gly Gly Gly Gly Gly Ala Ala Val Ser Gly Gly 180 185 190 gag gat gcg gtg gat gat aac tca tcc tcg gtt aac gaa ggt aac aat 624 Glu Asp Ala Val Asp Asp Asn Ser Ser Ser Val Asn Glu Gly Asn Asn 195 200 205 tgg agg agc agt tca cgg aag agg aaa gac gag gaa gga gaa gag caa 672 Trp Arg Ser Ser Ser Arg Lys Arg Lys Asp Glu Glu Gly Glu Glu Gln 210 215 220 gga gat gat aag gac gaa gat gcg tcg aat ttg aag aaa ccg cgt gtc 720 Gly Asp Asp Lys Asp Glu Asp Ala Ser Asn Leu Lys Lys Pro Arg Val 225 230 235 240 gtc tgg tct gtt gaa ttg cat cag cag ttt gtt gct gct gtt aat cag 768 Val Trp Ser Val Glu Leu His Gln Gln Phe Val Ala Ala Val Asn Gln 245 250 255 ctc ggc gtt gag aag gcg gtt cct aaa aag atc tta gag ctg atg aat 816 Leu Gly Val Glu Lys Ala Val Pro Lys Lys Ile Leu Glu Leu Met Asn 260 265 270 gtt cct ggt cta acc cga gaa aac gta gca agt cac ctc cag aaa tac 864 Val Pro Gly Leu Thr Arg Glu Asn Val Ala Ser His Leu Gln Lys Tyr 275 280 285 cgg ata tat cta aga cgg ctt gga ggg gta tcg cag cac caa ggc aat 912 Arg Ile Tyr Leu Arg Arg Leu Gly Gly Val Ser Gln His Gln Gly Asn 290 295 300 ctt aac aac tcg ttt atg acg ggt cag gat gcg agc ttc gga cct ctt 960 Leu Asn Asn Ser Phe Met Thr Gly Gln Asp Ala Ser Phe Gly Pro Leu 305 310 315 320 tcg aca ttg aat ggg ttt gat ctt caa gca cta gcc gtc aca ggt cag 1008 Ser Thr Leu Asn Gly Phe Asp Leu Gln Ala Leu Ala Val Thr Gly Gln 325 330 335 tta cct gca cag agt ctt gca cag ctt caa gcc gct ggt tta ggc cgg 1056 Leu Pro Ala Gln Ser Leu Ala Gln Leu Gln Ala Ala Gly Leu Gly Arg 340 345 350 cct gcg atg gtc tct aag tca ggt ttg ccg gtt tcc tcc att gtg gat 1104 Pro Ala Met Val Ser Lys Ser Gly Leu Pro Val Ser Ser Ile Val Asp 355 360 365 gag aga agc atc ttc agc ttt gac aac acg aaa aca aga ttt gga gaa 1152 Glu Arg Ser Ile Phe Ser Phe Asp Asn Thr Lys Thr Arg Phe Gly Glu 370 375 380 ggg ctt ggg cat cac ggg caa caa ccc caa cag caa cca cag atg aac 1200 Gly Leu Gly His His Gly Gln Gln Pro Gln Gln Gln Pro Gln Met Asn 385 390 395 400 tta ctt cac ggt gtc ccc acg ggt tta caa cag cag ctt cct atg ggt 1248 Leu Leu His Gly Val Pro Thr Gly Leu Gln Gln Gln Leu Pro Met Gly 405 410 415 aat cga atg agt att caa caa cag att gct gct gtt cga gct gga aat 1296 Asn Arg Met Ser Ile Gln Gln Gln Ile Ala Ala Val Arg Ala Gly Asn 420 425 430 agt gtt caa aac aac gga atg ctg atg cct cta gcg ggt cag cag tct 1344 Ser Val Gln Asn Asn Gly Met Leu Met Pro Leu Ala Gly Gln Gln Ser 435 440 445 ttg cct cgg gga cca ccg cct atg cta acc tct tcg caa tca tcc atc 1392 Leu Pro Arg Gly Pro Pro Pro Met Leu Thr Ser Ser Gln Ser Ser Ile 450 455 460 agg cag ccg atg tta tca aac cgc att tcc gag aga agt ggt ttc tct 1440 Arg Gln Pro Met Leu Ser Asn Arg Ile Ser Glu Arg Ser Gly Phe Ser 465 470 475 480 gga agg aac aat atc ccc gag agc agc aga gtg tta ccg aca agt tac 1488 Gly Arg Asn Asn Ile Pro Glu Ser Ser Arg Val Leu Pro Thr Ser Tyr 485 490 495 act aat ctc aca aca caa cac tca tca agc tcg atg cct tat aac aac 1536 Thr Asn Leu Thr Thr Gln His Ser Ser Ser Ser Met Pro Tyr Asn Asn 500 505 510 ttc caa cca gaa ctt ccc gtg aac agt ttc ccg ctg gca agt gca cca 1584 Phe Gln Pro Glu Leu Pro Val Asn Ser Phe Pro Leu Ala Ser Ala Pro 515 520 525 ggg ata tca gta ccg gtt cgg aaa gcc act tct tac cag gaa gag gtt 1632 Gly Ile Ser Val Pro Val Arg Lys Ala Thr Ser Tyr Gln Glu Glu Val 530 535 540 aac agc tcc gaa gcg ggt ttc att acg ccg agc tac gac atg ttc acc 1680 Asn Ser Ser Glu Ala Gly Phe Ile Thr Pro Ser Tyr Asp Met Phe Thr 545 550 555 560 acc aga cag aat gat tgg gat ctg agg aat att gga ata gcc ttt gac 1728 Thr Arg Gln Asn Asp Trp Asp Leu Arg Asn Ile Gly Ile Ala Phe Asp 565 570 575 tca cat cag gac tca gaa tcc gct gcg ttt tcc gct tca gaa gcc tac 1776 Ser His Gln Asp Ser Glu Ser Ala Ala Phe Ser Ala Ser Glu Ala Tyr 580 585 590 tct tct tcg tcc atg tca aga cac aac acg aca gtt gca gcc acc gag 1824 Ser Ser Ser Ser Met Ser Arg His Asn Thr Thr Val Ala Ala Thr Glu 595 600 605 cat ggc cga aac cac cag cag cca cca tcg gga atg gta cag cac cat 1872 His Gly Arg Asn His Gln Gln Pro Pro Ser Gly Met Val Gln His His 610 615 620 cag gtt tat gca gac gga aac ggt ggt tca gtg agg gtg aaa tca gag 1920 Gln Val Tyr Ala Asp Gly Asn Gly Gly Ser Val Arg Val Lys Ser Glu 625 630 635 640 aga gtg gct acg gat aca gca aca atg gcg ttt cac gag cag tat agt 1968 Arg Val Ala Thr Asp Thr Ala Thr Met Ala Phe His Glu Gln Tyr Ser 645 650 655 aat caa gaa gat ctt atg agc gca ctt ctt aag cag gtt tga 2010 Asn Gln Glu Asp Leu Met Ser Ala Leu Leu Lys Gln Val 660 665 24 669 PRT Arabidopsis thaliana 24 Met Met Asn Pro Ser His Gly Arg Gly Leu Gly Ser Ala Gly Gly Ser 1 5 10 15 Ser Ser Gly Arg Asn Gln Gly Gly Gly Gly Glu Thr Val Val Glu Met 20 25 30 Phe Pro Ser Gly Leu Arg Val Leu Val Val Asp Asp Asp Pro Thr Cys 35 40 45 Leu Met Ile Leu Glu Arg Met Leu Arg Thr Cys Leu Tyr Glu Val Thr 50 55 60 Lys Cys Asn Arg Ala Glu Met Ala Leu Ser Leu Leu Arg Lys Asn Lys 65 70 75 80 His Gly Phe Asp Ile Val Ile Ser Asp Val His Met Pro Asp Met Asp 85 90 95 Gly Phe Lys Leu Leu Glu His Val Gly Leu Glu Met Asp Leu Pro Val 100 105 110 Ile Met Met Ser Ala Asp Asp Ser Lys Ser Val Val Leu Lys Gly Val 115 120 125 Thr His Gly Ala Val Asp Tyr Leu Ile Lys Pro Val Arg Met Glu Ala 130 135 140 Leu Lys Asn Ile Trp Gln His Val Val Arg Lys Arg Arg Ser Glu Trp 145 150 155 160 Ser Val Pro Glu His Ser Gly Ser Ile Glu Glu Thr Gly Glu Arg Gln 165 170 175 Gln Gln Gln His Arg Gly Gly Gly Gly Gly Ala Ala Val Ser Gly Gly 180 185 190 Glu Asp Ala Val Asp Asp Asn Ser Ser Ser Val Asn Glu Gly Asn Asn 195 200 205 Trp Arg Ser Ser Ser Arg Lys Arg Lys Asp Glu Glu Gly Glu Glu Gln 210 215 220 Gly Asp Asp Lys Asp Glu Asp Ala Ser Asn Leu Lys Lys Pro Arg Val 225 230 235 240 Val Trp Ser Val Glu Leu His Gln Gln Phe Val Ala Ala Val Asn Gln 245 250 255 Leu Gly Val Glu Lys Ala Val Pro Lys Lys Ile Leu Glu Leu Met Asn 260 265 270 Val Pro Gly Leu Thr Arg Glu Asn Val Ala Ser His Leu Gln Lys Tyr 275 280 285 Arg Ile Tyr Leu Arg Arg Leu Gly Gly Val Ser Gln His Gln Gly Asn 290 295 300 Leu Asn Asn Ser Phe Met Thr Gly Gln Asp Ala Ser Phe Gly Pro Leu 305 310 315 320 Ser Thr Leu Asn Gly Phe Asp Leu Gln Ala Leu Ala Val Thr Gly Gln 325 330 335 Leu Pro Ala Gln Ser Leu Ala Gln Leu Gln Ala Ala Gly Leu Gly Arg 340 345 350 Pro Ala Met Val Ser Lys Ser Gly Leu Pro Val Ser Ser Ile Val Asp 355 360 365 Glu Arg Ser Ile Phe Ser Phe Asp Asn Thr Lys Thr Arg Phe Gly Glu 370 375 380 Gly Leu Gly His His Gly Gln Gln Pro Gln Gln Gln Pro Gln Met Asn 385 390 395 400 Leu Leu His Gly Val Pro Thr Gly Leu Gln Gln Gln Leu Pro Met Gly 405 410 415 Asn Arg Met Ser Ile Gln Gln Gln Ile Ala Ala Val Arg Ala Gly Asn 420 425 430 Ser Val Gln Asn Asn Gly Met Leu Met Pro Leu Ala Gly Gln Gln Ser 435 440 445 Leu Pro Arg Gly Pro Pro Pro Met Leu Thr Ser Ser Gln Ser Ser Ile 450 455 460 Arg Gln Pro Met Leu Ser Asn Arg Ile Ser Glu Arg Ser Gly Phe Ser 465 470 475 480 Gly Arg Asn Asn Ile Pro Glu Ser Ser Arg Val Leu Pro Thr Ser Tyr 485 490 495 Thr Asn Leu Thr Thr Gln His Ser Ser Ser Ser Met Pro Tyr Asn Asn 500 505 510 Phe Gln Pro Glu Leu Pro Val Asn Ser Phe Pro Leu Ala Ser Ala Pro 515 520 525 Gly Ile Ser Val Pro Val Arg Lys Ala Thr Ser Tyr Gln Glu Glu Val 530 535 540 Asn Ser Ser Glu Ala Gly Phe Ile Thr Pro Ser Tyr Asp Met Phe Thr 545 550 555 560 Thr Arg Gln Asn Asp Trp Asp Leu Arg Asn Ile Gly Ile Ala Phe Asp 565 570 575 Ser His Gln Asp Ser Glu Ser Ala Ala Phe Ser Ala Ser Glu Ala Tyr 580 585 590 Ser Ser Ser Ser Met Ser Arg His Asn Thr Thr Val Ala Ala Thr Glu 595 600 605 His Gly Arg Asn His Gln Gln Pro Pro Ser Gly Met Val Gln His His 610 615 620 Gln Val Tyr Ala Asp Gly Asn Gly Gly Ser Val Arg Val Lys Ser Glu 625 630 635 640 Arg Val Ala Thr Asp Thr Ala Thr Met Ala Phe His Glu Gln Tyr Ser 645 650 655 Asn Gln Glu Asp Leu Met Ser Ala Leu Leu Lys Gln Val 660 665 

What is claimed is:
 1. A transgenic plant with a modified flowering time or flowering period phenotype, which plant comprises a recombinant polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a nucleotide sequence encoding a polypeptide comprising a sequence selected from SEQ ID Nos. 2N, where N=1-12, or a complementary nucleotide sequence thereof; (b) a nucleotide sequence encoding a polypeptide comprising a conservatively substituted variant of a polypeptide of (a); (c) a nucleotide sequence comprising a sequence selected from those of SEQ ID Nos. 2N-1, where N=1-12, or a complementary nucleotide sequence thereof; (d) a nucleotide sequence comprising silent substitutions in a nucleotide sequence of (c); (e) a nucleotide sequence which hybridizes under stringent conditions to a nucleotide sequence of one or more of: (a), (b), (c), or (d); (f) a nucleotide sequence comprising at least 15 consecutive nucleotides of a sequence of any of (a)-(e); (g) a nucleotide sequence comprising a subsequence or fragment of any of (a)-(f), which subsequence or fragment encodes a polypeptide that modifies a flowering phenotype; (h) a nucleotide sequence having at least 40% sequence identity to a nucleotide sequence of any of (a)-(g); (i) a nucleotide sequence having at least 85% sequence identity to a nucleotide sequence of any of (a)-(g); (j) a nucleotide sequence which encodes a polypeptide having at least 40% sequence identity to a polypeptide of SEQ ID Nos. 2N, where N=1-12; (k) a nucleotide sequence which encodes a polypeptide having at least 85% sequence identity to a polypeptide of SEQ ID Nos. 2N, where N=1-12; and (l) a nucleotide sequence which encodes a polypeptide having at least 65% sequence identity to a conserved domain of a polypeptide of SEQ ID Nos. 2N, where N=1-12.
 2. The transgenic plant of claim 1, further comprising a constitutive, inducible, or tissue-active promoter operably linked to said nucleotide sequence.
 3. An isolated or recombinant polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a nucleotide sequence encoding a polypeptide comprising a sequence selected from SEQ ID Nos. 2N, where N=1-12, or a complementary nucleotide sequence thereof; (b) a nucleotide sequence encoding a polypeptide comprising a conservatively substituted variant of a polypeptide of (a); (c) a nucleotide sequence comprising a sequence selected from those of SEQ ID Nos. 2N-1, where N=1-12, or a complementary nucleotide sequence thereof; (d) a nucleotide sequence comprising silent substitutions in a nucleotide sequence of (c); (e) a nucleotide sequence which hybridizes under stringent conditions to a nucleotide sequence of one or more of: (a), (b), (c), or (d); (f) a nucleotide sequence comprising at least 15 consecutive nucleotides of a sequence of any of (a)-(e); (g) a nucleotide sequence comprising a subsequence or fragment of any of (a)-(f), which subsequence or fragment encodes a polypeptide having a biological activity that modifies a plant's flowering phenotype; (h) a nucleotide sequence having at least 40% sequence identity to a nucleotide sequence of any of (a)-(g); (i) a nucleotide sequence having at least 85% sequence identity to a nucleotide sequence of any of (a)-(g); (j) a nucleotide sequence which encodes a polypeptide having at least 40% sequence identity to a polypeptide of SEQ ID Nos. 2N, where N=1-12; (k) a nucleotide sequence which encodes a polypeptide having at least 85% sequence identity to a polypeptide of SEQ ID Nos. 2N, where N=1-12; and (l) a nucleotide sequence which encodes a conserved domain of a polypeptide having at least 65% sequence identity to a conserved domain of a polypeptide of SEQ ID Nos. 2N, where N=1-12.
 4. The isolated or recombinant polynucleotide of claim 3, further comprising a constitutive, inducible, or tissue-active promoter operably linked to the nucleotide sequence.
 5. A cloning or expression vector comprising the isolated or recombinant polynucleotide of claim
 3. 6. A cell comprising the cloning or expression vector of claim
 5. 7. A transgenic plant comprising the isolated or recombinant polynucleotide of claim
 3. 8. A composition comprising two or more different polynucleotides of claim
 3. 9. An isolated or recombinant polypeptide comprising a subsequence of at least about 15 contiguous amino acids encoded by the recombinant or isolated polynucleotide of claim
 3. 10. A plant ectopically expressing an isolated polypeptide of claim
 9. 11. A method for producing a plant having a modified flowering phenotype, the method comprising altering the expression of the isolated or recombinant polynucleotide of claim 3 or the expression levels or activity of a polypeptide of claim 9 in a plant, thereby producing a modified plant, and selecting the modified plant for an improved flowering phenotype thereby providing the modified plant with a modified flowering phenotype.
 12. A method of identifying a factor that is modulated by or interacts with a polypeptide encoded by a polynucleotide of claim 3, the method comprising: (a) expressing a polypeptide encoded by the polynucleotide in a plant; and (b) identifying at least one factor that is modulated by or interacts with the polypeptide.
 13. The method of claim 12, wherein the identifying is performed by detecting binding by the polypeptide to a promoter sequence, or detecting interactions between an additional protein and the polypeptide in a yeast two hybrid system.
 14. The method of claim 12, wherein the identifying is performed by detecting expression of a factor by hybridization to a microarray, subtractive hybridization or differential display.
 15. A method of identifying a molecule that modulates activity or expression of a polynucleotide or polypeptide of interest, the method comprising: (a) placing the molecule in contact with a plant comprising the polynucleotide or polypeptide encoded by the polynucleotide of claim 3; and, (b) monitoring one or more of: (i) expression level of the polynucleotide in the plant; (ii) expression level of the polypeptide in the plant; (iii) modulation of an activity of the polypeptide in the plant; or (iv) modulation of an activity of the polynucleotide in the plant.
 16. An integrated system, computer or computer readable medium comprising one or more character strings corresponding to a polynucleotide of claim 3, or to a polypeptide encoded by the polynucleotide.
 17. The integrated system, computer or computer readable medium of claim 16, further comprising a link between said one or more sequence strings to a modified plant flowering phenotype.
 18. A method of identifying a sequence similar or homologous to one or more polynucleotides of claim 3, or one or more polypeptides encoded by the polynucleotides, the method comprising: (a) providing a sequence database; and, (b) querying the sequence database with one or more target sequences corresponding to the one or more polynucleotides or to the one or more polypeptides to identify one or more sequence members of the database that display sequence similarity or homology to one or more of the one or more target sequences.
 19. The method of claim 18, wherein the querying comprises aligning one or more of the target sequences with one or more of the one or more sequence members in the sequence database.
 20. The method of claim 19, wherein the querying comprises identifying one or more of the one or more sequence members of the database that meet a user-selected identity criteria with one or more of the target sequences.
 21. The method of claim 18, further comprising linking the one or more of the polynucleotides of claim 3, or encoded polypeptides, to a modified plant flowering phenotype.
 22. A plant comprising altered expression levels of the isolated or recombinant polynucleotide of claim
 3. 23. A plant comprising altered expression levels or the activity of the isolated or recombinant polypeptide of claim
 9. 